Variant report

Variant	rs213955
Chromosome Location	chr7:117220861-117220862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1042077	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs10487368	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs10487369	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10953847	0.89[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs117243	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs11770639	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12533524	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12538252	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12673260	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1429566	0.90[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1469486	0.99[ASN][1000 genomes]
rs1557630	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1820871	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1896886	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1896887	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1896888	0.90[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2027944	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2027945	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2027946	0.81[ASN][1000 genomes]
rs2078753	0.95[ASN][1000 genomes]
rs2082056	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs213934	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs213935	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs213936	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs213937	0.88[ASN][1000 genomes]
rs213942	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs213943	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs213945	0.91[YRI][hapmap]
rs213946	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs213950	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs213953	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs213956	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs213957	0.98[ASN][1000 genomes]
rs213958	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs213961	0.96[ASN][1000 genomes]
rs213963	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs213964	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs213965	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs213966	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs213967	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs213968	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs213970	0.97[ASN][1000 genomes]
rs213971	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs213973	0.97[ASN][1000 genomes]
rs213974	0.97[ASN][1000 genomes]
rs2188159	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2237721	0.91[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap]
rs2237722	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2237723	0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2237724	0.90[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2237725	0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2283054	0.81[CHB][hapmap]
rs2283055	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2283056	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2283057	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2402204	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2402205	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2402228	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518873	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34456592	0.85[ASN][1000 genomes]
rs34683806	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34855237	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35388491	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35608825	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3757802	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs3808183	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs3808184	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3808185	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3808186	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4148686	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4148687	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4148688	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4148689	0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4148690	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4148691	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4148692	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4148696	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4148697	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4148698	0.91[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4148699	0.90[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4148703	0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4148706	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4148709	0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs4148711	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4148713	0.95[ASN][1000 genomes]
rs6466613	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6466614	0.97[ASN][1000 genomes]
rs6949974	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs6951141	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6957317	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6969138	0.90[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6977764	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6979652	0.96[ASN][1000 genomes]
rs718829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs725188	0.83[ASN][1000 genomes]
rs739378	0.88[ASN][1000 genomes]
rs756665	0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7786196	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7793127	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7803222	0.87[ASN][1000 genomes]
rs885993	0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs957461	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs980574	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889077	chr7:117129404-117238379	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv889078	chr7:117135025-117246315	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv889080	chr7:117176248-117238379	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv889081	chr7:117203417-117238379	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv889082	chr7:117203417-117246315	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv889083	chr7:117203417-117256374	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv889084	chr7:117212723-117246315	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv889085	chr7:117214089-117246315	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv889086	chr7:117214089-117252873	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs213955	PPP1R3A	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117208600-117232400	Weak transcription	Pancreas	Pancrea
2	chr7:117214000-117228000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr7:117214400-117228000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr7:117216800-117235600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:117217200-117226000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:117217400-117222000	Weak transcription	Fetal Intestine Large	intestine
7	chr7:117217400-117222800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:117218400-117228000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr7:117218800-117221800	Weak transcription	Fetal Intestine Small	intestine
10	chr7:117220400-117223000	Enhancers	A549	lung
11	chr7:117220600-117223200	Enhancers	Hela-S3	cervix

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