Variant report

Variant	rs12907338
Chromosome Location	chr15:59672765-59672766
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	chr15:59663703..59665247-chr15:59672295..59676019,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157470	Chromatin interaction
ENSG00000157483	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11071434	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071435	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11071438	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11071440	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11636899	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854940	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12372983	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12372986	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12908836	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12910391	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12913287	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1484282	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71480523	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs900828	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv934082	chr15:59608605-59733211	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv457175	chr15:59609753-59681214	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv569603	chr15:59609753-59681214	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv471246	chr15:59610743-59681214	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv904274	chr15:59623576-59689378	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv904275	chr15:59648633-59726610	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	n/a
8	nsv904276	chr15:59648633-59743010	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	n/a
9	nsv904277	chr15:59666992-59705005	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
10	nsv524569	chr15:59666992-59712427	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59665800-59674000	Weak transcription	Fetal Kidney	kidney
2	chr15:59665800-59675800	Weak transcription	Brain Hippocampus Middle	brain
3	chr15:59665800-59678400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:59665800-59680200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:59665800-59691800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:59666000-59674400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr15:59666000-59674800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:59666000-59676400	Weak transcription	Colon Smooth Muscle	Colon
9	chr15:59666000-59677000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr15:59666000-59678400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:59666000-59678400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:59666000-59678800	Weak transcription	Fetal Lung	lung
13	chr15:59666000-59680800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:59666200-59673200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr15:59666200-59674000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr15:59666200-59680400	Weak transcription	Fetal Stomach	stomach
17	chr15:59666200-59680600	Weak transcription	NHEK	skin
18	chr15:59666200-59681800	Weak transcription	Ovary	ovary
19	chr15:59666400-59680600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:59666800-59674000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:59667400-59672800	Weak transcription	Stomach Mucosa	stomach
22	chr15:59667400-59674800	Weak transcription	Fetal Heart	heart
23	chr15:59667400-59691800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:59667600-59673000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr15:59667600-59674200	Weak transcription	Liver	Liver
26	chr15:59670400-59675800	Weak transcription	GM12878-XiMat	blood
27	chr15:59670400-59685000	Weak transcription	Primary B cells from cord blood	blood
28	chr15:59670600-59672800	Weak transcription	Hela-S3	cervix
29	chr15:59670600-59676200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr15:59671200-59673600	Enhancers	Fetal Intestine Small	intestine
31	chr15:59671400-59673600	Enhancers	Fetal Intestine Large	intestine
32	chr15:59671600-59674800	Weak transcription	HepG2	liver
33	chr15:59671600-59675200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:59671800-59673000	Weak transcription	A549	lung
35	chr15:59672000-59673000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr15:59672200-59673000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr15:59672600-59672800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:59672600-59674400	Enhancers	Placenta	Placenta
39	chr15:59672600-59675200	Strong transcription	Aorta	Aorta

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