Variant report

Variant	rs2579552
Chromosome Location	chr2:96737083-96737084
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10183151	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs1030864	0.87[EUR][1000 genomes]
rs11680950	0.89[JPT][hapmap];0.89[YRI][hapmap]
rs11683523	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11687113	0.91[CEU][hapmap]
rs1168965	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1168968	0.81[CEU][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes]
rs1168970	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs1168972	0.87[EUR][1000 genomes]
rs1168974	0.81[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.87[EUR][1000 genomes]
rs1168975	0.82[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.87[EUR][1000 genomes]
rs1168976	0.81[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.87[EUR][1000 genomes]
rs11689832	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11695514	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs1724125	0.85[EUR][1000 genomes]
rs2140938	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2229169	0.91[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2301707	0.81[CEU][hapmap]
rs2312955	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2438972	0.92[CEU][hapmap]
rs2438978	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs2462774	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs2579519	0.91[CEU][hapmap]
rs2579549	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2579550	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2692893	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2692894	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2692934	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2692935	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2692936	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2692937	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2917662	0.90[EUR][1000 genomes]
rs2918916	0.87[EUR][1000 genomes]
rs2969491	0.87[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3111873	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3821051	0.81[CEU][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap]
rs4144055	1.00[YRI][hapmap]
rs4426564	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs4527246	0.92[CEU][hapmap]
rs4907288	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs4907299	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs6740563	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs7561198	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7604842	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs893173	0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1840487	chr2:96582807-96836512	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv870250	chr2:96610946-96739308	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv874672	chr2:96637870-96809331	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv874673	chr2:96647856-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv874674	chr2:96651163-96741944	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv1825266	chr2:96704118-96830753	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2579552	ADRA2B	cis	Nerve Tibial	GTEx
rs2579552	GPAT2	cis	Muscle Skeletal	GTEx
rs2579552	CIAO1	Cis_1M	lymphoblastoid	RTeQTL
rs2579552	FAHD2CP	cis	Muscle Skeletal	GTEx
rs2579552	GPAT2	cis	Adipose Subcutaneous	GTEx
rs2579552	ADRA2B	cis	Thyroid	GTEx
rs2579552	FAHD2CP	cis	lung	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96731600-96737200	Weak transcription	Spleen	Spleen
2	chr2:96734000-96737200	Weak transcription	Fetal Brain Male	brain
3	chr2:96734200-96738200	Weak transcription	Brain Angular Gyrus	brain
4	chr2:96734200-96749400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:96734400-96738600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:96734400-96758000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:96734800-96738000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:96735800-96738600	Enhancers	HSMM	muscle
9	chr2:96735800-96738800	Enhancers	Brain Hippocampus Middle	brain
10	chr2:96735800-96739000	Enhancers	Brain Anterior Caudate	brain
11	chr2:96735800-96739200	Enhancers	HSMMtube	muscle
12	chr2:96735800-96740200	Enhancers	Fetal Muscle Trunk	muscle
13	chr2:96735800-96740400	Enhancers	Fetal Muscle Leg	muscle
14	chr2:96736000-96737600	Enhancers	Brain Germinal Matrix	brain
15	chr2:96736000-96738600	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr2:96736600-96738600	Enhancers	Brain Cingulate Gyrus	brain
17	chr2:96736600-96739000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr2:96736800-96738000	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:96736800-96738600	Enhancers	Brain Substantia Nigra	brain
20	chr2:96737000-96738000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links