Variant report

Variant	rs3772638
Chromosome Location	chr3:134884473-134884474
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10804635	1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1159404	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs11712935	0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12636613	1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12636659	1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13063564	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13076510	0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs13087756	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1392918	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1404577	0.86[CHD][hapmap];0.90[JPT][hapmap]
rs1501195	0.83[MEX][hapmap]
rs1501205	1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1501206	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1501207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880531	0.81[CHD][hapmap]
rs2270882	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291989	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs3772637	0.80[CEU][hapmap]
rs3772640	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772647	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3772648	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821503	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4894286	0.83[MEX][hapmap]
rs4894287	0.83[MEX][hapmap]
rs7372088	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7373413	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs7620133	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7642038	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]
rs882058	0.85[CEU][hapmap]
rs940639	0.83[CHD][hapmap]
rs9822213	0.83[MEX][hapmap]
rs9845406	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9883173	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.94[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
rs3772638	CLDN18	cis	parietal	SCAN
rs3772638	EPHB1	cis	cerebellum	SCAN
rs3772638	UBA5	cis	parietal	SCAN
rs3772638	WDFY4	trans	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134867800-134884800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:134872800-134885000	Weak transcription	Brain Germinal Matrix	brain
3	chr3:134874800-134901800	Weak transcription	GM12878-XiMat	blood
4	chr3:134878200-134887800	Weak transcription	Spleen	Spleen
5	chr3:134879000-134884800	Weak transcription	Fetal Brain Male	brain
6	chr3:134879000-134887200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:134879000-134889600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:134879200-134888000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:134880400-134888400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:134880600-134885400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:134880600-134888200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:134880800-134888000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:134880800-134889400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:134880800-134889600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:134880800-134889800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:134881200-134891000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:134881800-134885600	Weak transcription	Fetal Brain Female	brain
18	chr3:134882400-134885400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:134883200-134887000	Weak transcription	Liver	Liver
20	chr3:134883600-134885800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:134883800-134886000	Enhancers	Brain Hippocampus Middle	brain
22	chr3:134884000-134884800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr3:134884000-134885600	Enhancers	Brain Angular Gyrus	brain
24	chr3:134884000-134886000	Enhancers	Brain Anterior Caudate	brain
25	chr3:134884000-134887400	Enhancers	Brain Cingulate Gyrus	brain
26	chr3:134884200-134885600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:134884200-134885800	Enhancers	Brain Substantia Nigra	brain
28	chr3:134884400-134885000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:134884400-134885800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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