Variant report

Variant	rs1967039
Chromosome Location	chr15:59654066-59654067
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59652101..59655720-chr15:59664711..59668394,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157483	Chromatin interaction
ENSG00000157470	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12438647	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12438936	0.87[EUR][1000 genomes]
rs1471746	0.87[EUR][1000 genomes]
rs16941344	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16941346	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1967040	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2414629	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28378088	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28406496	1.00[AMR][1000 genomes];0.87[EUR][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	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

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59623200-59662800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:59634800-59662600	Weak transcription	Colonic Mucosa	Colon
3	chr15:59637800-59662000	Weak transcription	Right Ventricle	heart
4	chr15:59638600-59654600	Weak transcription	Liver	Liver
5	chr15:59642600-59659400	Weak transcription	Ovary	ovary
6	chr15:59642800-59658600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:59643000-59656200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:59643000-59659400	Weak transcription	Fetal Intestine Small	intestine
9	chr15:59643600-59658800	Weak transcription	Fetal Intestine Large	intestine
10	chr15:59644800-59654400	Weak transcription	Osteobl	bone
11	chr15:59644800-59659400	Weak transcription	Right Atrium	heart
12	chr15:59645200-59656400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr15:59645200-59659200	Weak transcription	Fetal Heart	heart
14	chr15:59645200-59662000	Weak transcription	Psoas Muscle	Psoas
15	chr15:59645400-59659200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:59645400-59659400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr15:59646600-59662200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:59646800-59656400	Weak transcription	HUVEC	blood vessel
19	chr15:59646800-59662600	Weak transcription	Gastric	stomach
20	chr15:59647000-59662400	Weak transcription	Adipose Nuclei	Adipose
21	chr15:59647800-59659400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr15:59647800-59659400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:59648600-59658600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr15:59648600-59658600	Weak transcription	Small Intestine	intestine
25	chr15:59648600-59663200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:59648800-59662200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:59649000-59659200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:59649000-59663400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr15:59650400-59654400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:59650600-59658800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr15:59650600-59659400	Weak transcription	Aorta	Aorta
32	chr15:59650600-59659400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr15:59650600-59663400	Weak transcription	Fetal Stomach	stomach
34	chr15:59651200-59658000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr15:59652000-59659400	Weak transcription	Pancreas	Pancrea
36	chr15:59652400-59654400	Genic enhancers	A549	lung
37	chr15:59653000-59659200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr15:59653000-59659400	Weak transcription	Brain Angular Gyrus	brain
39	chr15:59653200-59654400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:59653200-59657600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:59653400-59655800	Strong transcription	Hela-S3	cervix
42	chr15:59653400-59656000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:59653400-59656000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:59653400-59656200	Weak transcription	Lung	lung
45	chr15:59653400-59656200	Weak transcription	NHDF-Ad	bronchial
46	chr15:59653400-59656400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:59653400-59657800	Weak transcription	Brain Substantia Nigra	brain
48	chr15:59653400-59658600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:59653400-59658600	Weak transcription	Brain Hippocampus Middle	brain
50	chr15:59653400-59658600	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links