Variant report

Variant	rs12876985
Chromosome Location	chr13:94773878-94773879
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10492634	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12428018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12429417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12429989	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12859264	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1333257	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1333259	0.81[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1333260	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7321727	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9561499	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9561500	0.90[CHB][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9561503	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933807	chr13:94187158-94845505	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv948455	chr13:94451368-94988900	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916640	chr13:94521959-95101443	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv533063	chr13:94560362-95101443	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv430599	chr13:94699399-94934930	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv933263	chr13:94711183-94897124	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv900924	chr13:94714981-94819307	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv1051276	chr13:94745995-94872494	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv526048	chr13:94767311-94880219	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv562754	chr13:94770794-94895346	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12876985	GPR180	cis	parietal	SCAN
rs12876985	GPR180	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94768000-94785800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr13:94772000-94774000	Weak transcription	Fetal Heart	heart
3	chr13:94772000-94774600	Weak transcription	Psoas Muscle	Psoas
4	chr13:94772000-94774800	Weak transcription	Stomach Mucosa	stomach
5	chr13:94772000-94775000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr13:94772000-94775800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr13:94772200-94776400	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr13:94772600-94774000	Weak transcription	Gastric	stomach
9	chr13:94772600-94774200	Enhancers	HepG2	liver
10	chr13:94772600-94775000	Enhancers	Fetal Intestine Large	intestine
11	chr13:94772600-94776200	Enhancers	Fetal Intestine Small	intestine
12	chr13:94772600-94778000	Enhancers	Liver	Liver
13	chr13:94773000-94774800	Enhancers	Small Intestine	intestine
14	chr13:94773200-94774400	Enhancers	HSMM	muscle
15	chr13:94773400-94774600	Weak transcription	Fetal Kidney	kidney
16	chr13:94773400-94780800	Weak transcription	Pancreas	Pancrea
17	chr13:94773600-94774600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr13:94773600-94774600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr13:94773600-94775200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr13:94773600-94775600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr13:94773600-94780600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr13:94773800-94774200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr13:94773800-94774800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr13:94773800-94774800	Enhancers	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links