Variant report

Variant	rs12035458
Chromosome Location	chr1:119977687-119977688
allele	C/T
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	MYC	chr1:119977668-119978042	MCF10A-Er-Src	breast:	n/a	n/a
2	E2F4	chr1:119977620-119977980	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
HSD3BP2	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10923815	0.90[EUR][1000 genomes]
rs10923817	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10923820	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023716	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12032036	0.86[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs12032901	0.84[AMR][1000 genomes]
rs12044792	0.85[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes]
rs12402935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403000	0.90[EUR][1000 genomes]
rs12403392	0.86[CHB][hapmap];0.87[JPT][hapmap];0.90[EUR][1000 genomes]
rs12404131	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12411080	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes]
rs1341012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1341016	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1361530	0.87[CHB][hapmap]
rs1417609	0.87[CHB][hapmap]
rs1417610	0.87[CHB][hapmap]
rs17023517	0.88[JPT][hapmap];0.90[EUR][1000 genomes]
rs17023641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1891031	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2050894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2854961	0.82[CHB][hapmap]
rs3765957	0.86[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes]
rs3795660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41443445	0.86[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes]
rs4659174	0.87[CHB][hapmap]
rs58322461	0.90[EUR][1000 genomes]
rs58496137	0.90[EUR][1000 genomes]
rs58498757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58657268	0.90[EUR][1000 genomes]
rs61331918	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6676988	0.93[EUR][1000 genomes]
rs6691943	0.86[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs6692175	0.93[AFR][1000 genomes]
rs72991418	0.90[EUR][1000 genomes]
rs7556598	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv917091	chr1:119688975-120023222	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv34089	chr1:119752112-120072961	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv1004662	chr1:119847447-120154798	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	esv2763647	chr1:119929442-120154798	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv946176	chr1:119960027-119989077	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:119974600-119980800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:119975200-119980600	Weak transcription	Fetal Intestine Large	intestine
3	chr1:119977400-119977800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:119977400-119978200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:119977400-119978200	Enhancers	HMEC	breast
6	chr1:119977600-119978000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:119977600-119978000	Enhancers	NHDF-Ad	bronchial
8	chr1:119977600-119978200	Enhancers	NHEK	skin

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