Variant report

Variant	rs12901016
Chromosome Location	chr15:42331214-42331215
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	chr15:42302667..42304179-chr15:42329977..42332936,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11629515	0.85[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11633848	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11634009	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11638234	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11857594	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs12898459	0.80[ASN][1000 genomes]
rs12904287	0.88[ASN][1000 genomes]
rs12914009	0.88[ASN][1000 genomes]
rs1622221	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1622949	0.85[CEU][hapmap]
rs1668555	0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs1668557	1.00[JPT][hapmap]
rs1668560	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1668561	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1668562	0.87[CEU][hapmap]
rs1668581	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1668582	1.00[JPT][hapmap]
rs1668583	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1668584	1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs1704362	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1704366	0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs1704370	0.87[CEU][hapmap]
rs1704373	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1704376	0.93[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1823552	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2598465	0.83[ASN][1000 genomes]
rs2598466	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2598467	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2665202	0.83[ASN][1000 genomes]
rs2665203	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2665205	0.82[EUR][1000 genomes]
rs2665207	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2665210	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2665211	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2724935	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2724937	0.85[ASN][1000 genomes]
rs2724939	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2724940	0.85[ASN][1000 genomes]
rs2724941	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2724942	0.82[EUR][1000 genomes]
rs2724944	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2724945	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35670495	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55638864	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs56171410	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7165532	0.82[ASN][1000 genomes]
rs7166079	0.84[ASN][1000 genomes]
rs7177034	1.00[YRI][hapmap]
rs7181618	0.88[ASN][1000 genomes]
rs937991	1.00[YRI][hapmap]
rs937992	1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv904130	chr15:42323591-42336018	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42326200-42337200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr15:42328000-42337400	Weak transcription	Fetal Intestine Small	intestine
3	chr15:42329000-42333600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:42329000-42335400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:42329000-42336600	Weak transcription	Spleen	Spleen
6	chr15:42330200-42339600	Weak transcription	Lung	lung
7	chr15:42330800-42333600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:42331000-42335000	Weak transcription	Pancreas	Pancrea
9	chr15:42331000-42337000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr15:42331000-42341000	Weak transcription	Esophagus	oesophagus

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