Variant report

Variant	rs17369792
Chromosome Location	chr21:47769296-47769297
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47741111..47743991-chr21:47768697..47770742,2	MCF-7	breast:
2	chr21:47769238..47772145-chr21:47780327..47783138,3	MCF-7	breast:
3	chr21:47769040..47771129-chr21:47781631..47783670,2	K562	blood:
4	chr21:47742148..47745488-chr21:47766251..47771392,4	K562	blood:

Variant related genes	Relation type
ENSG00000160299	Chromatin interaction
ENSG00000160298	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs12482343	1.00[ASN][1000 genomes]
rs12482741	1.00[ASN][1000 genomes]
rs12482903	1.00[ASN][1000 genomes]
rs12482934	1.00[ASN][1000 genomes]
rs12483577	1.00[ASN][1000 genomes]
rs13046028	1.00[ASN][1000 genomes]
rs13047784	1.00[ASN][1000 genomes]
rs16979054	1.00[ASN][1000 genomes]
rs17176534	1.00[ASN][1000 genomes]
rs17176737	1.00[ASN][1000 genomes]
rs17176779	1.00[ASN][1000 genomes]
rs17176793	1.00[ASN][1000 genomes]
rs17176800	1.00[ASN][1000 genomes]
rs17176905	1.00[ASN][1000 genomes]
rs17176926	1.00[ASN][1000 genomes]
rs17176974	1.00[ASN][1000 genomes]
rs17176988	1.00[ASN][1000 genomes]
rs17177030	1.00[ASN][1000 genomes]
rs17182739	1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs17182746	1.00[ASN][1000 genomes]
rs17183137	1.00[ASN][1000 genomes]
rs17183151	1.00[ASN][1000 genomes]
rs17183220	1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[ASN][1000 genomes]
rs17183368	1.00[ASN][1000 genomes]
rs17183473	1.00[ASN][1000 genomes]
rs17297798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17297961	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17298556	1.00[ASN][1000 genomes]
rs17300762	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs17300965	1.00[ASN][1000 genomes]
rs17302525	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs17372047	1.00[ASN][1000 genomes]
rs2212749	1.00[ASN][1000 genomes]
rs2839169	1.00[ASN][1000 genomes]
rs34268261	1.00[ASN][1000 genomes]
rs34500739	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56693387	1.00[ASN][1000 genomes]
rs59308388	1.00[ASN][1000 genomes]
rs59613587	1.00[ASN][1000 genomes]
rs60412264	1.00[ASN][1000 genomes]
rs60751239	1.00[ASN][1000 genomes]
rs61181882	1.00[ASN][1000 genomes]
rs61448213	1.00[ASN][1000 genomes]
rs61735811	1.00[ASN][1000 genomes]
rs61735814	1.00[ASN][1000 genomes]
rs61735815	1.00[ASN][1000 genomes]
rs61735817	1.00[ASN][1000 genomes]
rs61735818	1.00[ASN][1000 genomes]
rs61736728	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62212860	1.00[ASN][1000 genomes]
rs62214043	1.00[ASN][1000 genomes]
rs62214045	1.00[ASN][1000 genomes]
rs62214046	1.00[ASN][1000 genomes]
rs62214051	1.00[ASN][1000 genomes]
rs62214052	1.00[ASN][1000 genomes]
rs62214055	1.00[ASN][1000 genomes]
rs62215182	1.00[ASN][1000 genomes]
rs62215183	1.00[ASN][1000 genomes]
rs62215184	1.00[ASN][1000 genomes]
rs62215186	1.00[ASN][1000 genomes]
rs62215187	1.00[ASN][1000 genomes]
rs7278379	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs73909524	1.00[ASN][1000 genomes]
rs743346	1.00[ASN][1000 genomes]
rs8134519	1.00[ASN][1000 genomes]
rs9977340	1.00[ASN][1000 genomes]
rs9979331	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
2	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
3	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
4	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
5	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
6	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
7	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
8	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
9	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
10	nsv1059118	chr21:47398331-48090457	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
11	nsv544494	chr21:47398331-48090457	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
12	nsv934264	chr21:47401083-48090317	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
13	nsv1060978	chr21:47488073-47833640	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	n/a
14	nsv519904	chr21:47583506-47881309	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
15	nsv948761	chr21:47587940-48069930	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	n/a
16	nsv1055239	chr21:47591378-48090317	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
17	nsv544495	chr21:47591378-48090317	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
18	nsv933354	chr21:47609029-47851401	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a
19	nsv949706	chr21:47625544-48069930	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
20	nsv529496	chr21:47634193-48090317	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
21	nsv587975	chr21:47661235-47830843	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	n/a
22	nsv432159	chr21:47673247-47854392	Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	n/a
23	nsv527355	chr21:47678774-47863025	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	n/a
24	nsv914136	chr21:47681041-47900994	Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	n/a
25	nsv1064588	chr21:47700051-47788823	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	n/a
26	nsv544496	chr21:47700051-47788823	Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	n/a
27	nsv914137	chr21:47700498-47862624	Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	n/a
28	nsv914138	chr21:47700498-47866227	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	n/a
29	nsv914139	chr21:47706737-47786494	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
30	nsv914140	chr21:47712185-47866227	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	n/a
31	nsv933061	chr21:47746204-48031515	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	n/a
32	nsv1062858	chr21:47750884-48091343	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17369792	LOC653468	trans	multi-tissue	Pritchard
rs17369792	C21orf56	cis	multi-tissue	Pritchard
rs17369792	HRMT1L1	cis	multi-tissue	Pritchard
rs17369792	SPATC1L	cis	Artery Tibial	GTEx
rs17369792	SPATC1L	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47746000-47793000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr21:47746400-47770200	Weak transcription	Fetal Brain Male	brain
3	chr21:47746400-47789200	Strong transcription	Fetal Muscle Leg	muscle
4	chr21:47746400-47792000	Weak transcription	Fetal Heart	heart
5	chr21:47746400-47797200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr21:47747600-47787600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr21:47754000-47778400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr21:47754000-47781400	Strong transcription	Thymus	Thymus
9	chr21:47754000-47787400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr21:47754000-47787600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr21:47754200-47781000	Strong transcription	Fetal Thymus	thymus
12	chr21:47754200-47787800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr21:47755000-47775000	Weak transcription	Stomach Mucosa	stomach
14	chr21:47760400-47770200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr21:47763800-47778600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr21:47763800-47792400	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr21:47764000-47798000	Strong transcription	Fetal Stomach	stomach
18	chr21:47764200-47780000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr21:47764200-47780400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr21:47764200-47788000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr21:47764200-47792400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr21:47764200-47793200	Strong transcription	Dnd41	blood
23	chr21:47764200-47800200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr21:47764400-47771800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr21:47764400-47778600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr21:47764400-47778600	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr21:47764400-47780000	Strong transcription	Lung	lung
28	chr21:47764400-47797000	Strong transcription	Fetal Intestine Small	intestine
29	chr21:47764600-47774600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr21:47764600-47778600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr21:47764600-47778600	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr21:47764600-47778600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr21:47764600-47788600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr21:47764600-47790400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr21:47764800-47778400	Strong transcription	NHEK	skin
36	chr21:47764800-47784600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr21:47765000-47778600	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr21:47765200-47778400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr21:47765400-47774400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr21:47765400-47775400	Strong transcription	Brain Anterior Caudate	brain
41	chr21:47765400-47775800	Strong transcription	Primary B cells from cord blood	blood
42	chr21:47765400-47777600	Strong transcription	Primary B cells from peripheral blood	blood
43	chr21:47765400-47778200	Strong transcription	Colonic Mucosa	Colon
44	chr21:47765400-47778400	Strong transcription	NHLF	lung
45	chr21:47765400-47778600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr21:47765400-47778600	Strong transcription	Brain Germinal Matrix	brain
47	chr21:47765400-47778600	Strong transcription	HepG2	liver
48	chr21:47765400-47780000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr21:47765400-47780200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr21:47765400-47787600	Strong transcription	Primary T cells from cord blood	blood

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