Variant report

Variant	rs12537278
Chromosome Location	chr7:33340421-33340422
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1008582	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1009355	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs1019300	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10228013	0.82[ASN][1000 genomes]
rs10228439	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10230133	0.84[CHB][hapmap]
rs10233296	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10250045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10257361	0.94[CHB][hapmap]
rs10268074	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[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];0.98[ASN][1000 genomes]
rs10270013	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10278145	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10279081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10279513	0.81[EUR][1000 genomes]
rs1030029	0.89[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10951382	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10951383	1.00[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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11972278	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs12155105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12537836	0.80[EUR][1000 genomes]
rs12671191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13241465	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs1345307	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1345308	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1362228	1.00[JPT][hapmap]
rs1362230	1.00[JPT][hapmap]
rs1362231	0.83[CEU][hapmap];0.85[TSI][hapmap]
rs1362371	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1419898	0.83[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs1419900	0.95[JPT][hapmap]
rs1419909	0.95[JPT][hapmap]
rs1419914	0.95[JPT][hapmap]
rs1419916	0.88[CHD][hapmap];0.95[JPT][hapmap]
rs1419918	0.95[JPT][hapmap]
rs1419919	0.85[CHD][hapmap];0.95[JPT][hapmap]
rs1419921	0.81[JPT][hapmap]
rs1419927	0.83[CHD][hapmap]
rs1419928	0.85[CHB][hapmap]
rs1420147	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1420148	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs1420155	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1420158	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1420159	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap]
rs1544557	0.95[JPT][hapmap]
rs1548880	0.85[CHB][hapmap]
rs1592465	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1592466	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1592467	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1819826	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1833177	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1860600	0.95[JPT][hapmap]
rs1894810	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs1894873	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1969575	0.85[EUR][1000 genomes]
rs2024430	1.00[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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2058342	0.95[JPT][hapmap]
rs2392230	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2392231	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2392233	0.84[CHB][hapmap]
rs2392236	0.95[JPT][hapmap]
rs2893469	0.95[JPT][hapmap]
rs4141012	1.00[JPT][hapmap]
rs4236337	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs4509212	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs4510745	1.00[JPT][hapmap]
rs4582453	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs4607502	0.95[JPT][hapmap]
rs4720109	0.83[EUR][1000 genomes]
rs4720115	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4720120	0.95[JPT][hapmap]
rs4723261	0.88[CEU][hapmap];0.89[CHB][hapmap];0.85[EUR][1000 genomes]
rs4723272	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs4723288	0.80[CHD][hapmap]
rs5012441	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6462463	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6462464	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6462466	0.85[ASN][1000 genomes]
rs6462467	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6462477	0.80[CHD][hapmap]
rs6462479	1.00[JPT][hapmap]
rs6944623	0.81[EUR][1000 genomes]
rs6950434	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6960483	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs6976311	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6976753	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6977009	0.83[CHD][hapmap]
rs721533	0.89[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs721851	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs726463	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs726464	0.95[JPT][hapmap]
rs758779	0.80[CHD][hapmap]
rs758780	0.80[CHD][hapmap]
rs759396	0.86[CHB][hapmap]
rs764041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7778657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7778892	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7779367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7780194	0.88[CEU][hapmap];0.90[CHB][hapmap];0.89[GIH][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs7783610	0.90[CHB][hapmap]
rs7785012	0.95[JPT][hapmap]
rs7789344	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7791710	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7802888	0.84[CHB][hapmap]
rs7803065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7804723	0.95[JPT][hapmap]
rs7806637	0.80[EUR][1000 genomes]
rs7809540	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs964707	0.88[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs986553	0.89[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830943	chr7:33167106-33352759	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv606610	chr7:33218763-33486316	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1016416	chr7:33241443-33559477	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv916660	chr7:33272493-33506384	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1792546	chr7:33304218-33346932	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv887925	chr7:33304218-33361323	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3398087	chr7:33339761-33355341	Enhancers ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12537278	BBS9	cis	parietal	SCAN
rs12537278	INMT	cis	parietal	SCAN
rs12537278	C7orf41	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:33317000-33347600	Weak transcription	Pancreas	Pancrea
2	chr7:33328000-33354600	Weak transcription	Ovary	ovary
3	chr7:33334200-33357200	Weak transcription	Gastric	stomach
4	chr7:33339800-33340600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
5	chr7:33340000-33344000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:33340000-33346600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:33340000-33351200	Weak transcription	Left Ventricle	heart
8	chr7:33340000-33354400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr7:33340000-33358600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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