Variant report

Variant	rs17459362
Chromosome Location	chr6:128756393-128756394
allele	A/C
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	POLR2A	chr6:128755855-128756464	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr6:128755843-128756478	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:128755117..128756713-chr6:128761520..128763459,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228972	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10428737	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1339193	1.00[CEU][hapmap]
rs1612415	0.85[CEU][hapmap]
rs17055854	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17361665	0.81[EUR][1000 genomes]
rs1891146	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1891147	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1891148	0.92[EUR][1000 genomes]
rs4466261	0.92[CEU][hapmap]
rs58395468	0.95[EUR][1000 genomes]
rs59893653	0.95[EUR][1000 genomes]
rs66843622	0.95[EUR][1000 genomes]
rs6939023	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs722796	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs72974018	1.00[AFR][1000 genomes]
rs72974046	0.95[EUR][1000 genomes]
rs72974053	0.95[EUR][1000 genomes]
rs72974060	0.95[EUR][1000 genomes]
rs72974074	0.95[EUR][1000 genomes]
rs72974081	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7764930	1.00[CEU][hapmap]
rs953549	0.92[CEU][hapmap]
rs961292	1.00[CEU][hapmap];0.95[EUR][1000 genomes]

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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv830800	chr6:128710631-128878435	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128739800-128762600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr6:128740800-128777000	Weak transcription	Fetal Intestine Small	intestine
3	chr6:128743600-128759400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:128744600-128758800	Weak transcription	HSMM	muscle
5	chr6:128748200-128759600	Weak transcription	Fetal Stomach	stomach
6	chr6:128748600-128759200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr6:128748600-128759200	Weak transcription	Gastric	stomach
8	chr6:128748800-128759000	Weak transcription	Fetal Heart	heart
9	chr6:128748800-128759400	Weak transcription	Brain Anterior Caudate	brain
10	chr6:128749200-128758800	Weak transcription	Ovary	ovary
11	chr6:128752800-128758800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:128753200-128756600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:128753200-128756600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr6:128753200-128756600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:128753200-128777000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:128753400-128756400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr6:128753400-128756600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr6:128753400-128759600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr6:128753600-128759200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:128753800-128756600	Weak transcription	NHDF-Ad	bronchial
21	chr6:128754000-128756600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:128754600-128758200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:128754600-128759000	Weak transcription	Brain Angular Gyrus	brain
24	chr6:128754600-128759600	Weak transcription	HUVEC	blood vessel
25	chr6:128754800-128759000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:128754800-128761200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:128754800-128767000	Weak transcription	NHEK	skin
28	chr6:128755400-128756800	Enhancers	Brain Hippocampus Middle	brain
29	chr6:128755600-128759600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:128755800-128756600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:128756000-128756400	ZNF genes & repeats	Fetal Intestine Large	intestine
32	chr6:128756000-128756400	Enhancers	Left Ventricle	heart
33	chr6:128756000-128756400	Enhancers	Pancreas	Pancrea
34	chr6:128756000-128756800	Weak transcription	HepG2	liver
35	chr6:128756000-128758000	Weak transcription	Brain Substantia Nigra	brain
36	chr6:128756200-128757000	Enhancers	Fetal Thymus	thymus
37	chr6:128756200-128759000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:128756200-128759600	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links