Variant report

Variant	rs12622298
Chromosome Location	chr2:178450651-178450652
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10170667	0.87[CEU][hapmap];0.94[JPT][hapmap]
rs10196345	0.83[ASN][1000 genomes]
rs10201153	0.95[JPT][hapmap]
rs10497500	0.85[JPT][hapmap]
rs10497501	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10497502	0.85[JPT][hapmap]
rs10497503	0.89[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs10497508	0.85[JPT][hapmap]
rs10803909	0.81[EUR][1000 genomes]
rs10930798	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930799	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10930800	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10930801	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11684320	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11689550	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12463893	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12469386	0.89[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs12471741	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12612857	1.00[CEU][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12615367	0.95[JPT][hapmap]
rs12616093	0.95[JPT][hapmap]
rs12616443	0.81[EUR][1000 genomes]
rs12618139	0.90[JPT][hapmap]
rs12991272	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13000048	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs13004955	0.89[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs13013752	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13020788	0.89[CEU][hapmap]
rs13027299	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13403787	0.86[ASN][1000 genomes]
rs13404970	0.84[ASN][1000 genomes]
rs13417231	0.84[ASN][1000 genomes]
rs13420302	0.88[ASN][1000 genomes]
rs13430517	0.84[ASN][1000 genomes]
rs13432183	0.85[ASN][1000 genomes]
rs1348848	0.89[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1348849	0.89[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1348850	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs1374437	0.89[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1405713	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1453370	0.89[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1545364	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1548067	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16865203	0.85[JPT][hapmap]
rs16865291	0.85[JPT][hapmap]
rs16865328	0.95[JPT][hapmap]
rs16865331	0.95[JPT][hapmap]
rs1975543	0.90[EUR][1000 genomes]
rs2060929	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs2084233	0.89[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2121430	0.89[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs2166554	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2166558	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs2364854	0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs3213945	0.95[JPT][hapmap]
rs3769995	0.85[JPT][hapmap]
rs3769996	0.85[JPT][hapmap]
rs3769997	0.85[JPT][hapmap]
rs3770002	0.85[JPT][hapmap]
rs3813259	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs3902850	0.89[CEU][hapmap]
rs3927978	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4243388	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs4243390	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4341974	0.81[EUR][1000 genomes]
rs4528793	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4893822	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs4893823	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs4893825	0.89[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs4893950	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs4893957	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs4893959	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4893961	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4893962	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs4893965	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4893966	0.84[EUR][1000 genomes]
rs4893969	0.89[CEU][hapmap]
rs57562172	0.84[ASN][1000 genomes]
rs59666005	0.82[ASN][1000 genomes]
rs6710575	0.89[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs6734528	0.89[CEU][hapmap]
rs6736390	0.89[CEU][hapmap]
rs6742951	0.89[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs6761593	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7559521	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7565022	0.81[EUR][1000 genomes]
rs7587604	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs7591807	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs7604673	0.89[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7606235	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs8941	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9288004	0.84[ASN][1000 genomes]
rs9288005	0.84[ASN][1000 genomes]
rs952746	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][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	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2762964	chr2:178416394-178481818	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv3506731	chr2:178416851-178482200	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv3506732	chr2:178416851-178482200	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv3520312	chr2:178417102-178482200	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv3520313	chr2:178417102-178482200	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12622298	DKFZp451M2119	Cis_1M	lymphoblastoid	RTeQTL
rs12622298	TTC30B	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178445000-178457800	Weak transcription	Right Ventricle	heart
2	chr2:178449400-178452800	Enhancers	Fetal Muscle Leg	muscle
3	chr2:178449800-178450800	Enhancers	Liver	Liver
4	chr2:178449800-178451600	Enhancers	Colon Smooth Muscle	Colon
5	chr2:178450000-178450800	Enhancers	Fetal Brain Female	brain
6	chr2:178450000-178450800	Enhancers	Fetal Heart	heart
7	chr2:178450000-178450800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr2:178450000-178450800	Enhancers	Stomach Mucosa	stomach
9	chr2:178450000-178450800	Flanking Active TSS	HepG2	liver
10	chr2:178450000-178451200	Enhancers	Small Intestine	intestine
11	chr2:178450000-178451400	Enhancers	Left Ventricle	heart
12	chr2:178450200-178451200	Enhancers	Fetal Intestine Large	intestine
13	chr2:178450200-178451200	Enhancers	Rectal Smooth Muscle	rectum
14	chr2:178450400-178451400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr2:178450600-178451800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:178450600-178453600	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links