Variant report

Variant	rs6684527
Chromosome Location	chr1:174010052-174010053
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173991246..173993882-chr1:174009654..174011343,3	K562	blood:
2	chr1:173988269..173993375-chr1:174006872..174013712,7	MCF-7	breast:
3	chr1:173990435..173992484-chr1:174009792..174011488,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135870	Chromatin interaction
ENSG00000224977	Chromatin interaction

Extended variants
information (count: 189 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:186)

rs_ID	r²[population]
rs10127823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10494491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10912710	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10912716	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912717	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10912721	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11489771	0.80[EUR][1000 genomes]
rs12029025	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12058585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12060191	0.82[EUR][1000 genomes]
rs12060331	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12060401	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12063266	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12063818	0.82[EUR][1000 genomes]
rs12067580	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12069129	0.81[ASN][1000 genomes]
rs12071784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12072602	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12072905	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12077782	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12077812	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12083593	0.95[EUR][1000 genomes]
rs12085939	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12086019	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12086826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12087212	0.83[EUR][1000 genomes]
rs12089005	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12089405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12093885	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12562588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12562959	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12563156	0.87[EUR][1000 genomes]
rs12564858	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs12565352	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12565675	0.81[EUR][1000 genomes]
rs12565973	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12566022	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12566642	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12566643	0.82[EUR][1000 genomes]
rs12566651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12566842	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12567854	0.81[EUR][1000 genomes]
rs12567864	0.81[EUR][1000 genomes]
rs12737218	0.82[EUR][1000 genomes]
rs1321637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1322776	0.80[EUR][1000 genomes]
rs1322778	0.81[EUR][1000 genomes]
rs1322779	0.81[EUR][1000 genomes]
rs13375205	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1407126	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1407596	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1407597	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16828467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16846641	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16846667	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16846688	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1890881	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs1987871	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1987873	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2009083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2015075	0.82[EUR][1000 genomes]
rs2025241	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2227588	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes]
rs2227590	0.88[EUR][1000 genomes]
rs2227593	0.88[EUR][1000 genomes]
rs2227594	0.87[EUR][1000 genomes]
rs2227595	0.88[EUR][1000 genomes]
rs2227597	0.88[EUR][1000 genomes]
rs2227601	0.86[EUR][1000 genomes]
rs2227612	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs2295958	0.85[EUR][1000 genomes]
rs28595073	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2860841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2860845	0.93[EUR][1000 genomes]
rs2901784	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36013663	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3980286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41265242	0.81[EUR][1000 genomes]
rs41266044	0.82[EUR][1000 genomes]
rs4140468	0.82[EUR][1000 genomes]
rs4536054	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4652283	0.92[CEU][hapmap];0.84[CHB][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap]
rs4652298	0.92[CEU][hapmap];0.84[CHB][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs4652328	0.92[CEU][hapmap];0.84[CHB][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs56926540	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57849055	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57995528	0.82[EUR][1000 genomes]
rs58092103	0.83[EUR][1000 genomes]
rs59520434	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59960208	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60039606	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60265316	0.84[EUR][1000 genomes]
rs60551050	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61826771	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61826774	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61826777	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826779	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826780	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61826784	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826785	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826823	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826824	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826826	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826829	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61826831	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61827889	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61827901	0.82[EUR][1000 genomes]
rs61827902	0.82[EUR][1000 genomes]
rs61827903	0.82[EUR][1000 genomes]
rs61827904	0.84[EUR][1000 genomes]
rs61827905	0.82[EUR][1000 genomes]
rs61827928	0.81[EUR][1000 genomes]
rs61827930	0.81[EUR][1000 genomes]
rs61827932	0.81[EUR][1000 genomes]
rs61827933	0.81[EUR][1000 genomes]
rs61827934	0.84[EUR][1000 genomes]
rs61827935	0.81[EUR][1000 genomes]
rs61827936	0.85[EUR][1000 genomes]
rs61827938	0.88[EUR][1000 genomes]
rs61827956	0.88[EUR][1000 genomes]
rs61827957	0.87[EUR][1000 genomes]
rs61827959	0.89[EUR][1000 genomes]
rs61828571	0.82[EUR][1000 genomes]
rs61828575	0.82[EUR][1000 genomes]
rs61828576	0.82[EUR][1000 genomes]
rs61828577	0.82[EUR][1000 genomes]
rs61828578	0.82[EUR][1000 genomes]
rs61828580	0.82[EUR][1000 genomes]
rs61828583	0.82[EUR][1000 genomes]
rs61828584	0.82[EUR][1000 genomes]
rs61828587	0.82[EUR][1000 genomes]
rs61828589	0.82[EUR][1000 genomes]
rs61828590	0.82[EUR][1000 genomes]
rs61828591	0.82[EUR][1000 genomes]
rs61828595	0.82[EUR][1000 genomes]
rs61828895	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61828898	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61828899	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61828900	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61828901	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6425262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6425264	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6425266	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6425267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6425271	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425272	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6657380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6665720	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6665880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6668543	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6676307	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6677446	0.83[ASW][hapmap];0.95[LWK][hapmap];0.85[YRI][hapmap]
rs6680088	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6683276	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6688176	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6695887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6695940	0.87[EUR][1000 genomes]
rs6698123	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6702454	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6703547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs677	0.84[EUR][1000 genomes]
rs724416	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73039035	0.87[EUR][1000 genomes]
rs7523504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7525325	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs7528380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs7530661	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7547880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7549291	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs767053	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9283385	0.93[EUR][1000 genomes]
rs9286896	0.88[EUR][1000 genomes]
rs9425431	0.92[CEU][hapmap];0.84[CHB][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs9425433	0.92[CEU][hapmap];0.84[CHB][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs9425434	0.82[EUR][1000 genomes]
rs9425436	0.86[EUR][1000 genomes]
rs9425762	0.82[EUR][1000 genomes]
rs9425773	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9425775	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9425779	0.95[EUR][1000 genomes]
rs9425780	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs961148	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs965498	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9728376	0.98[EUR][1000 genomes];0.98[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	nsv916960	chr1:173907804-174080248	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv872551	chr1:173913804-174025660	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6684527	SERPINC1	cis	Thyroid	GTEx
rs6684527	SERPINC1	cis	lung	GTEx
rs6684527	SERPINC1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174000800-174010600	Weak transcription	HepG2	liver
2	chr1:174008200-174010200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:174009000-174010200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:174009000-174010200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr1:174009600-174010200	Enhancers	Brain Cingulate Gyrus	brain
6	chr1:174009600-174010200	Enhancers	Brain Hippocampus Middle	brain
7	chr1:174009600-174010200	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr1:174009600-174010400	Enhancers	Brain Anterior Caudate	brain
9	chr1:174009600-174010400	Enhancers	Brain Substantia Nigra	brain

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