Variant report

Variant	rs7642038
Chromosome Location	chr3:134877635-134877636
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10804635	0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1159404	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11712935	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs12636613	0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12636659	0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13063564	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13076510	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs13087756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1392918	0.86[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1404577	0.86[CHD][hapmap];0.90[JPT][hapmap]
rs1501205	0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1501206	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1501207	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1880531	0.81[CHD][hapmap]
rs2270882	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291989	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs3772638	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3772640	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772647	1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772648	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3821503	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7372088	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7373413	0.82[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7620133	0.90[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs882058	0.81[CEU][hapmap]
rs940639	0.83[CHD][hapmap]
rs9845406	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9883173	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[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	nsv1000277	chr3:134546080-134970837	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv877516	chr3:134689420-134918522	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv829731	chr3:134711713-134885064	Strong transcription Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7642038	EPHB1	cis	cerebellum	SCAN
rs7642038	WDFY4	trans	cerebellum	SCAN
rs7642038	CLDN18	cis	parietal	SCAN
rs7642038	UBA5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134823000-134880000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:134861000-134878200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:134861600-134880600	Weak transcription	Fetal Brain Female	brain
4	chr3:134867800-134884800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:134868000-134878400	Weak transcription	Brain Anterior Caudate	brain
6	chr3:134868000-134878400	Weak transcription	Fetal Brain Male	brain
7	chr3:134868600-134878600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:134868600-134883800	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:134869000-134878600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:134872800-134885000	Weak transcription	Brain Germinal Matrix	brain
11	chr3:134874400-134878600	Enhancers	Liver	Liver
12	chr3:134874800-134901800	Weak transcription	GM12878-XiMat	blood
13	chr3:134876600-134878400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:134877400-134878400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:134877400-134878400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:134877400-134879200	Enhancers	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links