Variant report

Variant	rs17770991
Chromosome Location	chr7:40847221-40847222
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	chr7:40847046-40848746	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
SUGCT	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1006376	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs10225209	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.94[ASN][1000 genomes]
rs10225445	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10226900	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10231324	0.93[ASN][1000 genomes]
rs10231545	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10235458	0.83[LWK][hapmap]
rs10243080	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.94[ASN][1000 genomes]
rs10252053	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10268219	0.91[ASW][hapmap];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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10272186	0.86[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs10272516	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10276001	0.92[ASN][1000 genomes]
rs10276629	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1029620	0.92[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1029621	0.85[LWK][hapmap]
rs10951639	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1115714	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1115715	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs1203569	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs1203570	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1203573	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs1203575	0.81[EUR][1000 genomes]
rs12666544	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs12701835	0.93[ASN][1000 genomes]
rs12701836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13237870	0.94[ASN][1000 genomes]
rs13240894	0.88[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1733483	0.85[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs17530165	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs17530213	0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs17621030	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.93[ASN][1000 genomes]
rs17688285	0.93[ASN][1000 genomes]
rs17688414	0.94[ASN][1000 genomes]
rs17770843	0.86[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs1921743	0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs1921745	0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs1921746	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1921747	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1921748	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1974547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302025	0.91[ASW][hapmap];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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302026	0.83[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs2329877	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs35146091	0.94[ASN][1000 genomes]
rs35570092	0.94[ASN][1000 genomes]
rs35628600	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35712272	0.94[ASN][1000 genomes]
rs35995194	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs36200804	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3815265	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4050963	0.93[ASN][1000 genomes]
rs4460274	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs59027414	0.82[ASN][1000 genomes]
rs62449401	0.94[ASN][1000 genomes]
rs62449405	0.85[ASN][1000 genomes]
rs62449407	0.85[ASN][1000 genomes]
rs68023334	0.94[ASN][1000 genomes]
rs723838	1.00[CEU][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs73125791	0.85[ASN][1000 genomes]
rs763714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7784052	0.84[ASN][1000 genomes]
rs7801192	0.93[ASN][1000 genomes]
rs7804009	0.94[ASN][1000 genomes]
rs7807596	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7808211	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs886831	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.94[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	nsv1030648	chr7:40218618-41032599	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830972	chr7:40814709-40945917	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv830973	chr7:40816419-40851594	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17770991	POLM	cis	parietal	SCAN
rs17770991	INHBA	cis	Nerve Tibial	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40835400-40847800	Weak transcription	Aorta	Aorta
2	chr7:40842400-40847600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:40842400-40847800	Weak transcription	HMEC	breast
4	chr7:40843600-40850000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:40844200-40848600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr7:40844400-40850600	Enhancers	HSMM	muscle
7	chr7:40844600-40850400	Enhancers	HSMMtube	muscle
8	chr7:40844800-40848200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:40845000-40847600	Weak transcription	NH-A	brain
10	chr7:40845000-40849600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:40845200-40847800	Weak transcription	Colonic Mucosa	Colon
12	chr7:40845400-40847800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr7:40845400-40847800	Weak transcription	Hela-S3	cervix
14	chr7:40845400-40850000	Enhancers	NHDF-Ad	bronchial
15	chr7:40845600-40847400	Weak transcription	NHLF	lung
16	chr7:40846400-40849200	Enhancers	Primary B cells from cord blood	blood
17	chr7:40846400-40850000	Enhancers	Primary B cells from peripheral blood	blood
18	chr7:40846600-40850200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:40847000-40848600	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr7:40847000-40849200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr7:40847000-40849800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr7:40847000-40849800	Enhancers	Osteobl	bone
23	chr7:40847200-40848200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:40847200-40848200	Enhancers	Ovary	ovary

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