Variant report

Variant	rs10487368
Chromosome Location	chr7:117140095-117140096
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 136 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10249651	0.81[CHB][hapmap]
rs1029396	0.86[CHB][hapmap]
rs1042077	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs10487365	0.81[CHB][hapmap]
rs10487369	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10953841	0.81[CHB][hapmap]
rs10953843	0.81[CHB][hapmap]
rs10953847	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs117243	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs11769166	0.85[CHB][hapmap]
rs11770639	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12333572	0.81[CHB][hapmap]
rs12533524	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12535986	0.86[CHB][hapmap]
rs12538252	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12673260	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13438309	0.88[ASN][1000 genomes]
rs1429566	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1557630	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1820871	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1896886	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1896887	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1896888	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2027944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2027945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2027946	0.82[ASN][1000 genomes]
rs2051718	0.86[CHB][hapmap]
rs2082056	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs213934	0.86[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap]
rs213935	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs213936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs213937	0.92[ASN][1000 genomes]
rs213942	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs213943	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs213946	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs213950	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs213953	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs213955	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]
rs213956	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs213963	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs213964	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs213965	0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs213966	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs213967	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs213968	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs213971	0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs2157946	0.86[CHB][hapmap]
rs2188158	0.91[ASN][1000 genomes]
rs2188159	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2188555	0.81[CHB][hapmap]
rs2237721	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs2237722	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2237723	0.92[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237724	0.85[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2237725	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2283054	0.91[CHB][hapmap]
rs2283055	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2283056	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2283057	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2402204	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2402205	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2402228	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2518873	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs254536	0.81[CHB][hapmap]
rs34456592	0.87[ASN][1000 genomes]
rs34683806	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34855237	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35388491	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35608825	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757802	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3808183	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs3808184	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3808185	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs3808186	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3926643	0.85[CHB][hapmap]
rs39312	0.81[CHB][hapmap]
rs39315	0.81[CHB][hapmap]
rs39317	0.81[CHB][hapmap]
rs39324	0.81[CHB][hapmap]
rs4148682	0.86[CHB][hapmap]
rs4148686	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4148687	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4148688	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4148689	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.95[MKK][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4148690	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4148691	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4148692	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4148696	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4148697	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4148698	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs4148699	0.85[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4148703	1.00[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4148706	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4148709	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs4148711	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs43025	0.81[CHB][hapmap]
rs43028	0.81[CHB][hapmap]
rs43029	0.81[CHB][hapmap]
rs43032	0.81[CHB][hapmap]
rs43034	0.81[CHB][hapmap]
rs43036	0.81[CHB][hapmap]
rs4727849	0.86[CHB][hapmap]
rs4727851	0.81[CHB][hapmap]
rs4730778	0.86[CHB][hapmap]
rs4730786	0.81[CHB][hapmap]
rs6466611	0.86[CHB][hapmap]
rs6466613	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6949974	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs6951141	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6957317	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6960356	0.86[CHB][hapmap]
rs6966838	0.90[CHB][hapmap]
rs6969138	0.85[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6977764	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6979185	0.81[CHB][hapmap]
rs713134	0.81[CHB][hapmap]
rs718829	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs725188	0.92[ASN][1000 genomes]
rs739378	0.90[ASN][1000 genomes]
rs739517	0.81[CHB][hapmap]
rs756665	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7784156	0.81[CHB][hapmap]
rs7786196	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7793127	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7803222	0.88[ASN][1000 genomes]
rs7805063	0.81[CHB][hapmap]
rs7808424	0.86[CHB][hapmap]
rs7810506	0.86[CHB][hapmap]
rs885993	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs957461	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9792104	0.81[CHB][hapmap]
rs980574	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs994996	0.81[CHB][hapmap]

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	nsv889076	chr7:117064625-117147547	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10487368	PPP1R3A	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117126800-117151200	Weak transcription	Pancreas	Pancrea
2	chr7:117129800-117144600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr7:117135200-117142200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr7:117135800-117141200	Weak transcription	Small Intestine	intestine
5	chr7:117136400-117141000	Weak transcription	Fetal Intestine Large	intestine
6	chr7:117139400-117140200	Enhancers	Fetal Intestine Small	intestine
7	chr7:117139600-117140200	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr7:117140000-117142000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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