Variant report

Variant	rs17393980
Chromosome Location	chr21:47971060-47971061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47876440..47878945-chr21:47970776..47973767,2	MCF-7	breast:
2	chr21:47964705..47967234-chr21:47968598..47971419,5	K562	blood:
3	chr21:47967795..47973717-chr21:47974569..47979109,7	K562	blood:

Variant related genes	Relation type
ENSG00000160305	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1023355	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11910493	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17302700	1.00[ASN][1000 genomes]
rs2330593	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2839260	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2839282	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2839293	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2839300	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2839323	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[ASN][1000 genomes]
rs2839324	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs2839338	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2839340	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2839341	1.00[ASN][1000 genomes]
rs2839348	0.91[ASN][1000 genomes]
rs2839361	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2839362	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2839366	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs4818845	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4819254	0.85[CEU][hapmap]
rs4819258	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4819261	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4819263	0.85[CEU][hapmap]
rs4819269	1.00[ASN][1000 genomes]
rs59699890	1.00[ASN][1000 genomes]
rs61657682	1.00[ASN][1000 genomes]
rs6518296	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7276841	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7277466	0.91[ASN][1000 genomes]
rs7278009	1.00[ASN][1000 genomes]
rs73379600	0.83[ASN][1000 genomes]
rs73379602	1.00[ASN][1000 genomes]
rs73381504	0.83[ASN][1000 genomes]
rs73381506	0.83[ASN][1000 genomes]
rs743347	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7510435	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8131943	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9977528	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9981272	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9981276	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9984082	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	nsv1056321	chr21:47835146-47973412	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
16	nsv917208	chr21:47836346-47988603	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
17	nsv1058397	chr21:47851176-48091343	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
18	nsv459312	chr21:47856106-47985655	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
19	nsv587998	chr21:47856106-47985655	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
20	nsv1065502	chr21:47865215-48091343	Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
21	nsv1056152	chr21:47875370-47979259	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
22	nsv1061442	chr21:47875370-48091343	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
23	nsv1059466	chr21:47894705-48096945	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	n/a
24	nsv1061185	chr21:47901250-48096945	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	n/a
25	nsv1057566	chr21:47915583-48029698	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	n/a
26	nsv587999	chr21:47941916-48103851	Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a
27	nsv1058589	chr21:47948030-48091343	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers 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	38 gene(s)	inside rSNPs	n/a
28	nsv1057643	chr21:47953820-48056600	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	n/a
29	nsv544497	chr21:47953820-48056600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer 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	36 gene(s)	inside rSNPs	n/a
30	nsv914147	chr21:47958657-47982652	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
31	nsv459313	chr21:47964259-47982652	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
32	nsv588000	chr21:47964259-47982652	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
33	nsv588001	chr21:47966504-47986001	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
34	nsv1056734	chr21:47970933-48096945	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17393980	LOC653468	trans	multi-tissue	Pritchard
rs17393980	DIP2A	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47943600-47990600	Strong transcription	Fetal Stomach	stomach
2	chr21:47947200-47975200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr21:47947600-47989000	Strong transcription	Dnd41	blood
4	chr21:47947600-47991000	Strong transcription	Fetal Muscle Leg	muscle
5	chr21:47948400-47971600	Strong transcription	Fetal Muscle Trunk	muscle
6	chr21:47948400-47993600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr21:47948600-47971400	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr21:47948600-47993200	Strong transcription	Fetal Intestine Large	intestine
9	chr21:47948800-47979400	Strong transcription	Liver	Liver
10	chr21:47949000-47979000	Strong transcription	Adipose Nuclei	Adipose
11	chr21:47949000-47988200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr21:47949000-47993600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr21:47949800-47991800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr21:47950000-47989200	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr21:47950000-47991000	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr21:47950200-47993200	Strong transcription	Stomach Smooth Muscle	stomach
17	chr21:47950400-47971800	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr21:47950400-47974400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr21:47952000-47978600	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr21:47953000-47974800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr21:47953000-47988200	Strong transcription	Gastric	stomach
22	chr21:47953000-47988600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr21:47953200-47971800	Strong transcription	Thymus	Thymus
24	chr21:47953200-47972000	Strong transcription	Ovary	ovary
25	chr21:47953200-47983400	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr21:47953200-47988400	Strong transcription	Fetal Intestine Small	intestine
27	chr21:47953200-47993000	Strong transcription	Osteobl	bone
28	chr21:47953400-47972000	Strong transcription	Brain Angular Gyrus	brain
29	chr21:47953400-47988000	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr21:47954400-47973000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr21:47955800-47972000	Strong transcription	Rectal Smooth Muscle	rectum
32	chr21:47956000-47978800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr21:47956200-48001800	Weak transcription	Stomach Mucosa	stomach
34	chr21:47957000-47978200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr21:47957200-47972400	Strong transcription	HepG2	liver
36	chr21:47959200-47983400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr21:47960000-47979200	Weak transcription	Right Atrium	heart
38	chr21:47960600-47972000	Strong transcription	Right Ventricle	heart
39	chr21:47960600-47974800	Strong transcription	Left Ventricle	heart
40	chr21:47961200-47971800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr21:47961600-47992800	Strong transcription	Brain Hippocampus Middle	brain
42	chr21:47964600-47988400	Strong transcription	Brain Germinal Matrix	brain
43	chr21:47965000-47972400	Strong transcription	Brain Anterior Caudate	brain
44	chr21:47965000-47972600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr21:47965000-47978200	Strong transcription	Fetal Lung	lung
46	chr21:47965200-47991200	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr21:47965600-47972000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr21:47965800-47972000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr21:47965800-47988600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr21:47965800-47993400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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