Variant report

Variant	rs513311
Chromosome Location	chr2:31625610-31625611
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:31610791..31613346-chr2:31624556..31626809,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158125	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs206797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs206799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs206801	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs206802	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs206809	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs206810	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs206813	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs206814	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs206815	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs206817	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs206818	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs206819	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs206828	0.86[ASN][1000 genomes]
rs206833	0.83[ASN][1000 genomes]
rs206850	0.83[AMR][1000 genomes]
rs206856	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes]
rs206857	0.86[JPT][hapmap]
rs473935	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes]
rs528551	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs561525	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949028	chr2:31502801-31665108	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv456030	chr2:31598823-31820256	Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv456041	chr2:31598823-31820256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv581269	chr2:31598823-31820256	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv998853	chr2:31601455-31858961	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1005565	chr2:31603134-31868877	Genic enhancers Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1007179	chr2:31616112-31835410	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1005032	chr2:31616112-31867450	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs513311	NHSL1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31548000-31634600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:31565200-31633000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:31574600-31636600	Weak transcription	Colonic Mucosa	Colon
4	chr2:31598400-31639000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:31599600-31636600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:31618000-31627000	Strong transcription	Fetal Intestine Small	intestine
7	chr2:31620000-31627600	Strong transcription	Duodenum Mucosa	Duodenum
8	chr2:31620800-31627400	Strong transcription	Liver	Liver
9	chr2:31623400-31625800	Enhancers	Hela-S3	cervix
10	chr2:31623400-31626200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:31623400-31628000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:31623600-31626000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:31623600-31626000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:31623600-31626000	Enhancers	NHDF-Ad	bronchial
15	chr2:31623800-31625800	Enhancers	Osteobl	bone
16	chr2:31623800-31626000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:31623800-31626000	Enhancers	NHLF	lung
18	chr2:31623800-31626200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr2:31624000-31626000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr2:31624000-31626200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:31624000-31626200	Enhancers	Placenta	Placenta
22	chr2:31624200-31626000	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr2:31624400-31626200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:31624400-31626200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:31624600-31625800	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr2:31624600-31625800	Enhancers	HMEC	breast
27	chr2:31624800-31626000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:31625200-31626200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr2:31625400-31625800	Genic enhancers	Fetal Intestine Large	intestine
30	chr2:31625400-31625800	Enhancers	NHEK	skin
31	chr2:31625400-31626000	Enhancers	NH-A	brain
32	chr2:31625400-31626200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:31625400-31626400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:31625400-31627600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:31625400-31627600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:31625400-31628400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:31625600-31626200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:31625600-31627600	Enhancers	A549	lung
39	chr2:31625600-31627800	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links