Variant report

Variant	rs11589200
Chromosome Location	chr1:171779108-171779109
allele	C/G
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	STAT3	chr1:171779002-171779355	MCF10A-Er-Src	breast:	n/a	chr1:171779211-171779220
2	CEBPB	chr1:171779060-171779371	MCF-7	breast:	n/a	n/a
3	FOS	chr1:171779025-171779387	MCF10A-Er-Src	breast:	n/a	chr1:171779211-171779220 chr1:171779213-171779224
4	STAT3	chr1:171778991-171779512	MCF10A-Er-Src	breast:	n/a	chr1:171779211-171779220
5	STAT3	chr1:171778973-171779357	MCF10A-Er-Src	breast:	n/a	chr1:171779211-171779220
6	MYC	chr1:171778985-171779363	MCF10A-Er-Src	breast:	n/a	chr1:171779212-171779221
7	FOS	chr1:171778939-171779403	MCF10A-Er-Src	breast:	n/a	chr1:171779211-171779220 chr1:171779213-171779224
8	MYC	chr1:171778970-171779296	MCF10A-Er-Src	breast:	n/a	chr1:171779212-171779221
9	FOS	chr1:171778980-171779408	MCF10A-Er-Src	breast:	n/a	chr1:171779211-171779220 chr1:171779213-171779224
10	FOS	chr1:171778984-171779409	MCF10A-Er-Src	breast:	n/a	chr1:171779211-171779220 chr1:171779213-171779224
11	CEBPB	chr1:171779073-171779267	HepG2	liver:	n/a	n/a
12	STAT3	chr1:171778989-171779339	MCF10A-Er-Src	breast:	n/a	chr1:171779211-171779220
13	CEBPB	chr1:171779037-171779362	Hela-S3	cervix:	n/a	n/a
14	CEBPB	chr1:171779076-171779262	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171749390..171751584-chr1:171778813..171780615,2	MCF-7	breast:
2	chr1:171777006..171779367-chr1:171820349..171823318,2	K562	blood:

Variant related genes	Relation type
ENSG00000252134	TF binding region
ENSG00000010165	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10158220	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10158235	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10158943	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10159080	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10489253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753190	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10753195	0.92[ASN][1000 genomes]
rs10753196	0.92[ASN][1000 genomes]
rs10753197	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10753198	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1079820	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798637	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10798657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798658	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10798661	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798679	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913633	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10913639	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10913651	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913730	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10913743	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10913799	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10913803	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11579138	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11580187	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11585645	0.82[ASN][1000 genomes]
rs11588649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589823	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11590059	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11590829	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807195	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12022693	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12031686	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12035109	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12036580	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12057976	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12063769	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12562644	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12723938	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12735285	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12754084	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12755791	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1555101	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1555102	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17597528	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17597542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2206541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2206542	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2232804	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2232809	0.87[ASN][1000 genomes]
rs2232811	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294719	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294720	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294721	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294722	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2421912	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2421913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34219132	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35738870	0.87[EUR][1000 genomes]
rs4292987	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55739261	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59592673	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6425416	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425417	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425422	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425428	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425435	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425436	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425437	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425440	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425441	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6656814	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6657803	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6658116	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6658730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658980	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6659621	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665727	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6668165	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6674810	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6675011	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6678230	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6682147	0.92[ASN][1000 genomes]
rs6685030	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6689108	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6689213	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6690544	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695736	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6698366	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6698467	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6698892	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6700184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6702424	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs732304	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs732305	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7517546	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7517555	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7520688	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs752514	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7525313	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7537173	0.93[ASN][1000 genomes]
rs7537770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537931	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7537935	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7539505	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541128	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7542691	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7545100	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7549347	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7550603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552369	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7556602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs764179	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs764180	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs909959	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];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	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171767800-171781800	Weak transcription	Thymus	Thymus
2	chr1:171768400-171785600	Weak transcription	Gastric	stomach
3	chr1:171770200-171794600	Weak transcription	Primary T cells from cord blood	blood
4	chr1:171770600-171784800	Weak transcription	Primary B cells from cord blood	blood
5	chr1:171773000-171796000	Weak transcription	Pancreas	Pancrea
6	chr1:171775000-171787000	Weak transcription	Left Ventricle	heart
7	chr1:171775400-171779800	Weak transcription	Brain Anterior Caudate	brain
8	chr1:171775400-171783800	Weak transcription	Brain Angular Gyrus	brain
9	chr1:171777200-171780000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:171777600-171780000	Enhancers	HMEC	breast
11	chr1:171777800-171786200	Weak transcription	Brain Substantia Nigra	brain
12	chr1:171777800-171786400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:171777800-171786400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:171778600-171779800	Enhancers	NHEK	skin
15	chr1:171778600-171780000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:171778800-171779400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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