Variant report

Variant	rs1883588
Chromosome Location	chr6:2374888-2374889
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:2373039..2375063-chr6:2375225..2378148,2	K562	blood:
2	chr6:2368647..2371784-chr6:2373502..2376486,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WRNIP1-34	chr6:2370339-2376003	NONHSAT106653

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1016500	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10793836	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11242767	0.81[ASN][1000 genomes]
rs11759415	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12197998	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12213061	0.81[ASN][1000 genomes]
rs13218890	0.81[ASN][1000 genomes]
rs1883586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883590	0.81[ASN][1000 genomes]
rs2073002	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2092403	0.81[ASN][1000 genomes]
rs4281006	0.82[ASN][1000 genomes]
rs4354194	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4413658	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4959183	0.82[ASN][1000 genomes]
rs4959649	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4959655	0.82[ASN][1000 genomes]
rs4959656	0.82[ASN][1000 genomes]
rs4959657	0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4959660	0.81[ASN][1000 genomes]
rs4959664	0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs56024732	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6907369	0.82[ASN][1000 genomes]
rs6920321	0.82[ASN][1000 genomes]
rs6925653	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6940450	0.82[ASN][1000 genomes]
rs7449538	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs764343	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs764344	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9503152	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9503158	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9503160	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9503162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
2	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
5	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
6	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	esv3356254	chr6:2374553-2378751	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1883588	SERPINB1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2344400-2377400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr6:2352400-2376400	Weak transcription	HSMMtube	muscle
3	chr6:2353800-2376400	Weak transcription	Pancreas	Pancrea
4	chr6:2354200-2376400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:2356200-2382200	Weak transcription	Aorta	Aorta
6	chr6:2356600-2382800	Weak transcription	Psoas Muscle	Psoas
7	chr6:2360400-2379600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:2362400-2376800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:2362400-2391800	Weak transcription	Fetal Intestine Small	intestine
10	chr6:2362400-2397200	Weak transcription	Liver	Liver
11	chr6:2362800-2397200	Weak transcription	Left Ventricle	heart
12	chr6:2367400-2377200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:2370200-2389000	Weak transcription	Esophagus	oesophagus
14	chr6:2370400-2376800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:2371400-2376600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links