Variant report

Variant	rs260538
Chromosome Location	chr15:29981554-29981555
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10152681	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11073218	0.90[JPT][hapmap]
rs12438925	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1383315	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1480503	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1552077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1679647	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1871678	0.97[ASN][1000 genomes]
rs2032	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2229518	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2337167	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs260528	0.84[ASN][1000 genomes]
rs260529	0.84[ASN][1000 genomes]
rs260531	0.89[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs260532	0.89[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs260533	0.89[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs260534	0.89[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs260535	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2878893	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2878905	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4073316	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4362339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4779670	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4780258	0.91[ASN][1000 genomes]
rs4780259	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4780260	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs6495914	0.81[ASN][1000 genomes]
rs7176476	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7176594	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7180387	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs767514	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs785445	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs8027827	0.82[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	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv903747	chr15:29361126-30008977	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv995038	chr15:29744279-30366124	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1038495	chr15:29825859-30351687	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv542293	chr15:29825859-30351687	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv832944	chr15:29861062-30082057	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv832945	chr15:29932599-30123721	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:29969200-29992000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:29972800-29989200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr15:29973600-29989600	Weak transcription	Fetal Muscle Leg	muscle
4	chr15:29977800-29996200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:29978000-29983200	Weak transcription	HMEC	breast
6	chr15:29978400-29982800	Weak transcription	NH-A	brain
7	chr15:29978400-29983000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr15:29978400-29983200	Weak transcription	HSMMtube	muscle
9	chr15:29978400-29990400	Weak transcription	NHLF	lung
10	chr15:29978600-29983200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:29978600-29983200	Weak transcription	HUVEC	blood vessel
12	chr15:29978600-29983200	Weak transcription	Osteobl	bone
13	chr15:29978600-29983400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr15:29978600-29984800	Weak transcription	NHDF-Ad	bronchial
15	chr15:29978800-29983200	Weak transcription	HSMM	muscle
16	chr15:29979200-29988400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr15:29979600-29981600	Enhancers	Esophagus	oesophagus
18	chr15:29979600-29983000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr15:29979800-29982800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:29979800-29993000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr15:29980200-29981800	Enhancers	Stomach Mucosa	stomach
22	chr15:29980200-29982600	Weak transcription	A549	lung
23	chr15:29980200-29983000	Weak transcription	HepG2	liver
24	chr15:29980800-29982000	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr15:29980800-29982800	Weak transcription	Liver	Liver
26	chr15:29980800-29983200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:29980800-29989800	Weak transcription	Brain Substantia Nigra	brain
28	chr15:29980800-29989800	Weak transcription	Fetal Kidney	kidney
29	chr15:29980800-29996400	Weak transcription	Colonic Mucosa	Colon
30	chr15:29981000-29990400	Weak transcription	Lung	lung
31	chr15:29981000-29990600	Weak transcription	Fetal Intestine Large	intestine
32	chr15:29981000-29994400	Weak transcription	Fetal Intestine Small	intestine
33	chr15:29981200-29982800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:29981200-29983000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr15:29981200-29989600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:29981200-29993000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr15:29981400-29981600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:29981400-29982800	Weak transcription	Pancreas	Pancrea
39	chr15:29981400-29983200	Weak transcription	Gastric	stomach
40	chr15:29981400-29991800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr15:29981400-29994800	Weak transcription	K562	blood
42	chr15:29981400-29996400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links