Variant report

Variant	rs7176309
Chromosome Location	chr15:58767482-58767483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr15:58767115-58767497	GM19099	blood:	n/a	n/a
2	POLR2A	chr15:58766763-58769315	ECC-1	luminal epithelium:	n/a	n/a
3	TCF12	chr15:58767446-58768914	ECC-1	luminal epithelium:	n/a	n/a
4	MAX	chr15:58767003-58768523	ECC-1	luminal epithelium:	n/a	n/a
5	FOXM1	chr15:58767475-58769019	ECC-1	luminal epithelium:	n/a	n/a
6	NFIC	chr15:58767169-58769128	ECC-1	luminal epithelium:	n/a	n/a
7	FOXM1	chr15:58767471-58768621	ECC-1	luminal epithelium:	n/a	n/a
8	EP300	chr15:58766874-58769086	ECC-1	luminal epithelium:	n/a	chr15:58767982-58767998
9	NFIC	chr15:58767059-58767493	GM12878	blood:	n/a	n/a
10	RUNX3	chr15:58766844-58767541	GM12878	blood:	n/a	n/a
11	NFIC	chr15:58767424-58769150	ECC-1	luminal epithelium:	n/a	n/a
12	BCLAF1	chr15:58766975-58767520	GM12878	blood:	n/a	n/a
13	TCF12	chr15:58767353-58768831	ECC-1	luminal epithelium:	n/a	n/a
14	RUNX3	chr15:58766906-58767552	GM12878	blood:	n/a	n/a
15	MTA3	chr15:58766749-58767519	GM12878	blood:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58767133..58770014-chr15:58770584..58772843,2	MCF-7	breast:

No data

Variant related genes	Relation type
ALDH1A2	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12593736	1.00[YRI][hapmap]
rs12913605	1.00[YRI][hapmap]
rs17190580	1.00[YRI][hapmap]
rs6494009	1.00[YRI][hapmap]
rs6494011	1.00[YRI][hapmap]
rs7162603	1.00[YRI][hapmap]
rs7169623	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042201	chr15:58520746-58780710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv904267	chr15:58699010-58769583	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1047048	chr15:58701400-58784800	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3362898	chr15:58705732-58850860	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv457173	chr15:58731567-58779039	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv569600	chr15:58731567-58779039	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1043041	chr15:58744505-58876327	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv904268	chr15:58763678-58803225	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58743800-58770400	Enhancers	Fetal Thymus	thymus
2	chr15:58759400-58768400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:58759400-58770400	Enhancers	Placenta	Placenta
4	chr15:58760400-58770200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:58763000-58769400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:58764000-58770200	Enhancers	Fetal Muscle Leg	muscle
7	chr15:58764000-58770200	Enhancers	Thymus	Thymus
8	chr15:58764600-58769600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:58764600-58769600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr15:58764600-58770200	Enhancers	Spleen	Spleen
11	chr15:58764800-58769600	Enhancers	HSMMtube	muscle
12	chr15:58765000-58767600	Enhancers	HepG2	liver
13	chr15:58765000-58767800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr15:58765000-58768200	Enhancers	Lung	lung
15	chr15:58765000-58768400	Enhancers	Stomach Mucosa	stomach
16	chr15:58765000-58769400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:58765000-58769400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:58765000-58769600	Enhancers	Duodenum Mucosa	Duodenum
19	chr15:58765000-58769600	Enhancers	Right Atrium	heart
20	chr15:58765000-58769800	Enhancers	Adipose Nuclei	Adipose
21	chr15:58765000-58769800	Enhancers	Pancreas	Pancrea
22	chr15:58765000-58770000	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr15:58765000-58770400	Enhancers	Primary hematopoietic stem cells	blood
24	chr15:58765000-58770600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:58765000-58770600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:58765400-58769000	Weak transcription	Psoas Muscle	Psoas
27	chr15:58765400-58769200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr15:58765600-58768200	Weak transcription	Fetal Stomach	stomach
29	chr15:58765600-58768800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr15:58765600-58769000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr15:58765600-58770400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:58765800-58767600	Weak transcription	Fetal Lung	lung
33	chr15:58765800-58769600	Enhancers	HUVEC	blood vessel
34	chr15:58765800-58770000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:58765800-58770200	Enhancers	Primary T cells fromperipheralblood	blood
36	chr15:58765800-58770200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr15:58765800-58770200	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr15:58765800-58770400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr15:58766000-58767600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr15:58766000-58767600	Weak transcription	Brain Anterior Caudate	brain
41	chr15:58766000-58767600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr15:58766000-58768000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr15:58766000-58768200	Enhancers	NH-A	brain
44	chr15:58766000-58768400	Enhancers	HMEC	breast
45	chr15:58766000-58769800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr15:58766000-58770000	Enhancers	Primary T cells from cord blood	blood
47	chr15:58766000-58770400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr15:58766200-58767600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr15:58766200-58767600	Weak transcription	Esophagus	oesophagus
50	chr15:58766200-58767800	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links