Variant report

Variant	rs17562686
Chromosome Location	chr5:74668589-74668590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:74668241-74668912	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
COL4A3BP	TF binding region
ENSG00000242198	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10515198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11742194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11746245	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749414	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17244848	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17244855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17648288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3756558	0.85[LWK][hapmap];1.00[YRI][hapmap]
rs3761738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3761740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5744625	1.00[YRI][hapmap]
rs5744707	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882192	chr5:74641707-74707762	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74656400-74669800	Weak transcription	Ovary	ovary
2	chr5:74656400-74670400	Weak transcription	Right Ventricle	heart
3	chr5:74656400-74673600	Weak transcription	Psoas Muscle	Psoas
4	chr5:74656400-74673600	Weak transcription	Small Intestine	intestine
5	chr5:74656400-74673600	Weak transcription	Spleen	Spleen
6	chr5:74656400-74674000	Weak transcription	Brain Germinal Matrix	brain
7	chr5:74656400-74674800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr5:74656400-74674800	Weak transcription	Brain Substantia Nigra	brain
9	chr5:74656400-74676800	Weak transcription	Fetal Brain Male	brain
10	chr5:74656400-74687200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:74656400-74725600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:74656600-74670600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr5:74656600-74675600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr5:74656600-74675800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:74656600-74675800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr5:74656600-74676800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr5:74656600-74677200	Weak transcription	Aorta	Aorta
18	chr5:74656600-74694800	Weak transcription	Brain Angular Gyrus	brain
19	chr5:74656800-74669600	Weak transcription	Hela-S3	cervix
20	chr5:74656800-74670200	Weak transcription	HepG2	liver
21	chr5:74656800-74670400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr5:74656800-74676200	Weak transcription	Colonic Mucosa	Colon
23	chr5:74656800-74731400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr5:74657400-74674800	Weak transcription	A549	lung
25	chr5:74657600-74673600	Weak transcription	Lung	lung
26	chr5:74657800-74668600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr5:74657800-74668800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr5:74657800-74669400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr5:74657800-74708000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr5:74658000-74674800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr5:74658400-74668600	Weak transcription	Adipose Nuclei	Adipose
32	chr5:74658400-74673200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr5:74658600-74669600	Weak transcription	Brain Anterior Caudate	brain
34	chr5:74658600-74673200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr5:74658600-74674800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr5:74658600-74674800	Weak transcription	Fetal Kidney	kidney
37	chr5:74658800-74669400	Weak transcription	HSMMtube	muscle
38	chr5:74659000-74668600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:74659000-74668600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:74659000-74668600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:74659000-74668800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr5:74659000-74669200	Weak transcription	Fetal Brain Female	brain
43	chr5:74659000-74674600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr5:74659200-74668600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr5:74659200-74668600	Weak transcription	Dnd41	blood
46	chr5:74659200-74669800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr5:74659200-74670200	Weak transcription	Fetal Intestine Small	intestine
48	chr5:74659200-74674800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:74659400-74668800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr5:74659400-74669800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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