Variant report

Variant	rs17300762
Chromosome Location	chr21:47894724-47894725
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47894138..47896421-chr21:47897185..47899846,2	K562	blood:
2	chr21:47878656..47882894-chr21:47894260..47898635,4	K562	blood:
3	chr21:47874840..47880520-chr21:47886599..47894853,12	K562	blood:
4	chr21:47893839..47896328-chr21:48054252..48056582,2	K562	blood:
5	chr21:47893343..47896013-chr21:47906883..47909575,2	K562	blood:

Variant related genes	Relation type
ENSG00000160310	Chromatin interaction
ENSG00000160305	Chromatin interaction
ENSG00000223692	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10222184	1.00[ASN][1000 genomes]
rs1054691	1.00[ASN][1000 genomes]
rs17297798	1.00[ASN][1000 genomes]
rs17297961	1.00[ASN][1000 genomes]
rs17298556	1.00[ASN][1000 genomes]
rs17300965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17302525	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[TSI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305503	1.00[ASN][1000 genomes]
rs17369792	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]
rs17372047	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105495	1.00[ASN][1000 genomes]
rs2839326	1.00[GIH][hapmap]
rs2839353	0.87[CEU][hapmap]
rs2839370	1.00[ASN][1000 genomes]
rs2839373	1.00[ASW][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs2839376	1.00[ASW][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs34268261	1.00[ASN][1000 genomes]
rs34500739	1.00[ASN][1000 genomes]
rs59308388	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60412264	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60955061	1.00[ASN][1000 genomes]
rs61735811	1.00[ASN][1000 genomes]
rs61735814	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61735815	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61735817	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61735818	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61736728	1.00[ASN][1000 genomes]
rs7278379	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7349012	1.00[ASN][1000 genomes]
rs73909524	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743346	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941794	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:28 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	esv2762115	chr21:47885139-47895430	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
28	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17300762	TJP1	trans	lymphoblastoid	seeQTL
rs17300762	SPATC1L	cis	Artery Tibial	GTEx
rs17300762	CD79B	trans	lymphoblastoid	seeQTL
rs17300762	SPATC1L	cis	Skin Sun Exposed Lower leg	GTEx
rs17300762	HRMT1L1	cis	multi-tissue	Pritchard
rs17300762	VNN1	trans	lymphoblastoid	seeQTL
rs17300762	LOC653468	trans	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47880000-47900200	Weak transcription	Esophagus	oesophagus
2	chr21:47880000-47900400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr21:47880000-47905800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr21:47880000-47916800	Weak transcription	Aorta	Aorta
5	chr21:47880200-47900000	Weak transcription	Colonic Mucosa	Colon
6	chr21:47880200-47902800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr21:47880200-47903200	Weak transcription	Stomach Mucosa	stomach
8	chr21:47880200-47909400	Weak transcription	A549	lung
9	chr21:47880200-47911600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr21:47880200-47916600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr21:47880400-47896800	Weak transcription	Fetal Lung	lung
12	chr21:47880400-47898800	Weak transcription	HSMM	muscle
13	chr21:47880400-47906600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr21:47880400-47908800	Weak transcription	Fetal Brain Male	brain
15	chr21:47880400-47908800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr21:47880400-47909200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr21:47880400-47909200	Weak transcription	NHLF	lung
18	chr21:47880400-47909400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr21:47880400-47916600	Weak transcription	Fetal Kidney	kidney
20	chr21:47880400-47916600	Weak transcription	HSMMtube	muscle
21	chr21:47880400-47918000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr21:47880400-47918200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr21:47880400-47931200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr21:47880800-47902600	Weak transcription	Brain Angular Gyrus	brain
25	chr21:47882000-47898800	Weak transcription	Fetal Brain Female	brain
26	chr21:47882200-47898800	Weak transcription	Fetal Heart	heart
27	chr21:47882400-47900600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr21:47883200-47905200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr21:47883400-47903200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr21:47884600-47899400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr21:47884800-47899000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr21:47884800-47906000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr21:47885200-47898600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr21:47885200-47899600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr21:47885600-47899000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr21:47886200-47906800	Weak transcription	Hela-S3	cervix
37	chr21:47889600-47897000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr21:47889600-47903400	Weak transcription	Osteobl	bone
39	chr21:47889600-47906800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr21:47889600-47918200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr21:47889800-47895200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr21:47889800-47896200	Weak transcription	Fetal Intestine Small	intestine
43	chr21:47889800-47896400	Weak transcription	Dnd41	blood
44	chr21:47889800-47896600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr21:47889800-47898800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr21:47889800-47899000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr21:47889800-47899800	Weak transcription	Brain Germinal Matrix	brain
48	chr21:47889800-47905000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr21:47889800-47906200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr21:47889800-47907600	Weak transcription	NH-A	brain

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