Variant report

Variant	rs6657380
Chromosome Location	chr1:174009024-174009025
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173988269..173993375-chr1:174006872..174013712,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224977	Chromatin interaction
ENSG00000135870	Chromatin interaction

Extended variants
information (count: 155 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:152)

rs_ID	r²[population]
rs10127823	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10494491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912702	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10912710	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10912716	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912717	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10912721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11489771	0.83[EUR][1000 genomes]
rs12029025	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12058585	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12060191	0.84[EUR][1000 genomes]
rs12060331	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12060401	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12063266	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12063818	0.84[EUR][1000 genomes]
rs12067580	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12069129	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12071784	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12072602	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12072905	0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12077782	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12077812	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12083593	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12085939	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12086019	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12086826	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12087212	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12089005	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12089405	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12093885	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12562588	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12562959	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12563156	0.85[EUR][1000 genomes]
rs12564858	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12565352	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12565973	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12566022	0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12566642	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12566651	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12566842	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1321637	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1322779	0.83[EUR][1000 genomes]
rs13375205	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1407126	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1407596	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1407597	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16828467	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16846641	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16846667	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16846688	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1890881	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1987871	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1987873	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2009083	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2025241	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2227588	0.85[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs2227590	0.91[EUR][1000 genomes]
rs2227593	0.91[EUR][1000 genomes]
rs2227594	0.90[EUR][1000 genomes]
rs2227595	0.86[EUR][1000 genomes]
rs2227597	0.91[EUR][1000 genomes]
rs2227601	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2227612	0.84[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs2295958	0.87[EUR][1000 genomes]
rs28595073	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2860841	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2860845	0.90[EUR][1000 genomes]
rs2901784	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36013663	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3980286	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4536054	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4652283	0.84[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs4652298	0.84[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs4652328	0.84[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs56926540	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57849055	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57995528	0.84[EUR][1000 genomes]
rs58092103	0.81[EUR][1000 genomes]
rs59520434	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59960208	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60039606	0.81[ASN][1000 genomes]
rs60265316	0.82[EUR][1000 genomes]
rs60551050	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61826771	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61826774	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61826777	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826779	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826780	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61826784	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826785	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826823	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826824	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826826	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826829	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61826831	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61827889	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61827904	0.82[EUR][1000 genomes]
rs61827934	0.82[EUR][1000 genomes]
rs61827936	0.83[EUR][1000 genomes]
rs61827938	0.86[EUR][1000 genomes]
rs61827956	0.91[EUR][1000 genomes]
rs61827957	0.85[EUR][1000 genomes]
rs61827959	0.87[EUR][1000 genomes]
rs61828895	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61828898	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61828899	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61828900	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61828901	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6425262	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6425264	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6425266	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6425267	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6425271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425272	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6661182	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6665720	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6665880	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6668543	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6676307	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6680088	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6683276	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6684527	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688176	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6695887	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6695940	0.90[EUR][1000 genomes]
rs6698123	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6702454	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6703547	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs677	0.82[EUR][1000 genomes]
rs724416	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73039035	0.85[EUR][1000 genomes]
rs7523504	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7525325	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs7528380	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7530661	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7547880	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7549291	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs767053	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9283385	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9286896	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9425431	0.84[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs9425433	0.84[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs9425434	0.84[EUR][1000 genomes]
rs9425436	0.86[EUR][1000 genomes]
rs9425762	0.84[EUR][1000 genomes]
rs9425773	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9425775	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9425779	0.93[EUR][1000 genomes]
rs9425780	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs961148	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs965498	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9728376	1.00[AMR][1000 genomes];1.00[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6657380	SERPINC1	cis	Esophagus Mucosa	GTEx
rs6657380	SERPINC1	cis	Thyroid	GTEx
rs6657380	SERPINC1	cis	lung	GTEx
rs6657380	SERPINC1	cis	Muscle Skeletal	GTEx
rs6657380	SERPINC1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174000200-174009600	Weak transcription	NHLF	lung
2	chr1:174000800-174010600	Weak transcription	HepG2	liver
3	chr1:174008200-174009200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:174008200-174010200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:174009000-174010200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:174009000-174010200	Enhancers	Muscle Satellite Cultured Cells	--

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