Variant report

Variant	rs12622834
Chromosome Location	chr2:173538547-173538548
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	chr2:173534977..173536584-chr2:173536820..173539280,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11895461	0.80[CEU][hapmap]
rs11898565	0.91[CEU][hapmap]
rs11902830	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12052642	0.90[AFR][1000 genomes]
rs12615889	0.87[ASN][1000 genomes]
rs12622335	0.86[ASN][1000 genomes]
rs13384307	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13427921	0.84[TSI][hapmap]
rs16860794	0.87[ASN][1000 genomes]
rs16860795	0.87[ASN][1000 genomes]
rs16860796	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860798	0.87[ASN][1000 genomes]
rs16860809	0.95[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs2054162	0.84[ASN][1000 genomes]
rs2054163	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2084731	0.87[ASN][1000 genomes]
rs2084732	0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs3816536	0.91[CEU][hapmap]
rs4313941	0.86[ASN][1000 genomes]
rs4470304	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4972514	0.87[ASN][1000 genomes]
rs4972515	0.82[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4972516	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4972849	0.87[ASN][1000 genomes]
rs4972850	0.95[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs4972851	0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs59103702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61556691	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6716527	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6733953	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6743273	1.00[ASW][hapmap];0.96[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs6757567	0.92[AFR][1000 genomes]
rs733331	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs7590282	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv583665	chr2:173460640-173643087	Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12622834	UBR3	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173536400-173538600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:173536400-173538600	Enhancers	NHEK	skin
3	chr2:173536400-173538800	Enhancers	Muscle Satellite Cultured Cells	--
4	chr2:173536400-173539200	Enhancers	Fetal Intestine Large	intestine
5	chr2:173536400-173539600	Enhancers	Fetal Intestine Small	intestine
6	chr2:173536600-173538600	Enhancers	Osteobl	bone
7	chr2:173536800-173538800	Enhancers	HMEC	breast
8	chr2:173536800-173539000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:173536800-173539400	Enhancers	Duodenum Mucosa	Duodenum
10	chr2:173537400-173538600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:173537400-173542000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:173537600-173538600	Enhancers	HepG2	liver
13	chr2:173537600-173539600	Enhancers	Fetal Muscle Leg	muscle
14	chr2:173537800-173538600	Weak transcription	HSMMtube	muscle
15	chr2:173537800-173539600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:173538000-173539000	Enhancers	Placenta	Placenta
17	chr2:173538000-173539200	Weak transcription	Adipose Nuclei	Adipose
18	chr2:173538000-173539200	Weak transcription	Liver	Liver
19	chr2:173538200-173538600	Weak transcription	Fetal Heart	heart
20	chr2:173538200-173539000	Enhancers	A549	lung
21	chr2:173538200-173539200	Weak transcription	Stomach Mucosa	stomach
22	chr2:173538200-173539200	Weak transcription	NHLF	lung
23	chr2:173538200-173541800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:173538400-173539400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:173538400-173539400	Enhancers	Hela-S3	cervix
26	chr2:173538400-173541800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links