Variant report

Variant	rs59960208
Chromosome Location	chr1:173998776-173998777
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173988271..173993423-chr1:173996333..174006451,14	MCF-7	breast:
2	chr1:173989990..173993460-chr1:173995713..174001470,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135870	Chromatin interaction
ENSG00000224977	Chromatin interaction

Extended variants
information (count: 156 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs10127823	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10494491	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10912702	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10912710	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912716	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912717	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10912721	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11489771	0.84[EUR][1000 genomes]
rs12029025	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12058585	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12060191	0.85[EUR][1000 genomes]
rs12060331	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12060401	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12063266	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12063818	0.85[EUR][1000 genomes]
rs12067580	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12069129	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12071784	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12072602	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12072905	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12077782	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12077812	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12083593	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12085939	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12086019	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12086826	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12087212	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12089005	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12089405	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12093885	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12562588	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12562959	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12563156	0.86[EUR][1000 genomes]
rs12565352	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12565973	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12566022	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12566642	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12566651	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12566842	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1321637	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1322778	0.80[EUR][1000 genomes]
rs1322779	0.84[EUR][1000 genomes]
rs13375205	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1407126	0.82[ASN][1000 genomes]
rs1407596	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1407597	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16828467	0.84[ASN][1000 genomes]
rs16846641	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846667	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16846688	0.82[ASN][1000 genomes]
rs1987871	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1987872	0.81[ASN][1000 genomes]
rs1987873	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2009083	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2025241	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2227588	0.86[EUR][1000 genomes]
rs2227590	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2227593	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2227594	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2227595	0.87[EUR][1000 genomes]
rs2227597	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2227601	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2227612	0.84[EUR][1000 genomes]
rs2295958	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28595073	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2860841	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2860845	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2901784	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36013663	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3980286	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4536054	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4652283	0.82[EUR][1000 genomes]
rs4652298	0.85[EUR][1000 genomes]
rs4652328	0.85[EUR][1000 genomes]
rs56926540	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57849055	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57995528	0.85[EUR][1000 genomes]
rs58092103	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59520434	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60039606	0.82[ASN][1000 genomes]
rs60265316	0.83[EUR][1000 genomes]
rs60551050	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826771	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61826774	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826777	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826779	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826780	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61826784	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826785	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61826823	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61826824	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61826826	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61826829	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61826831	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61827889	0.85[ASN][1000 genomes]
rs61827928	0.80[EUR][1000 genomes]
rs61827930	0.80[EUR][1000 genomes]
rs61827932	0.80[EUR][1000 genomes]
rs61827933	0.80[EUR][1000 genomes]
rs61827934	0.83[EUR][1000 genomes]
rs61827935	0.80[EUR][1000 genomes]
rs61827936	0.84[EUR][1000 genomes]
rs61827938	0.87[EUR][1000 genomes]
rs61827956	0.92[EUR][1000 genomes]
rs61827957	0.86[EUR][1000 genomes]
rs61827959	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61828895	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61828898	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61828899	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61828900	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61828901	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6425262	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6425264	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425266	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6425267	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425271	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425272	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6657380	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6661182	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6665720	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6665880	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6668543	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676307	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6680088	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6683276	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6684527	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6688176	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6695887	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6695940	0.91[EUR][1000 genomes]
rs6698123	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6702454	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6703547	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs677	0.83[EUR][1000 genomes]
rs724416	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73039035	0.86[EUR][1000 genomes]
rs7523504	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7528380	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7530661	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7547880	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7549291	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs767053	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9283385	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9286896	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9425431	0.85[EUR][1000 genomes]
rs9425433	0.85[EUR][1000 genomes]
rs9425434	0.85[EUR][1000 genomes]
rs9425436	0.87[EUR][1000 genomes]
rs9425762	0.85[EUR][1000 genomes]
rs9425779	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9425780	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs961148	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs965498	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9728376	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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
rs59960208	SERPINC1	cis	Esophagus Mucosa	GTEx
rs59960208	SERPINC1	cis	lung	GTEx
rs59960208	SERPINC1	cis	Thyroid	GTEx
rs59960208	SERPINC1	cis	Muscle Skeletal	GTEx
rs59960208	SERPINC1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173992200-173999800	Weak transcription	NHLF	lung
2	chr1:173992800-173999800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:173993200-173999600	Weak transcription	A549	lung
4	chr1:173998200-173999800	Weak transcription	HepG2	liver
5	chr1:173998200-174002600	Weak transcription	Fetal Stomach	stomach
6	chr1:173998400-173999600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:173998600-173999000	Weak transcription	K562	blood

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