Variant report

Variant	rs10031777
Chromosome Location	chr4:48498290-48498291
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10018344	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10029732	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10029785	0.81[JPT][hapmap]
rs10030853	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10049761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.81[EUR][1000 genomes]
rs10938534	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10938537	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11728565	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11734019	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11737677	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11933919	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11945562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12503599	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12506098	0.86[EUR][1000 genomes]
rs12645501	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12645951	0.81[JPT][hapmap]
rs13108474	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13113370	0.81[EUR][1000 genomes]
rs13119041	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap]
rs13119504	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13127730	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13138269	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13151534	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1472967	0.81[JPT][hapmap]
rs1507862	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1507865	0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs1712768	0.86[EUR][1000 genomes]
rs1712772	0.81[EUR][1000 genomes]
rs17575720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17656010	0.88[ASN][1000 genomes]
rs17656040	0.80[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17656076	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17656094	0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1876469	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2089503	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2102397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs2291474	0.81[JPT][hapmap]
rs2291475	0.81[JPT][hapmap]
rs2292231	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2354312	0.83[EUR][1000 genomes]
rs2354348	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28470767	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2940324	0.80[EUR][1000 genomes]
rs2945330	0.84[EUR][1000 genomes]
rs3107022	0.85[EUR][1000 genomes]
rs34558821	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34635008	0.87[EUR][1000 genomes]
rs392187	0.81[JPT][hapmap]
rs404445	0.81[JPT][hapmap]
rs411261	0.81[JPT][hapmap]
rs421833	0.81[JPT][hapmap]
rs4536901	0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs4695391	0.87[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs59686413	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62311296	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6447640	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6447645	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6447647	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6447651	0.81[EUR][1000 genomes]
rs6811148	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6816010	0.81[JPT][hapmap]
rs6818954	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6819159	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6821277	0.81[JPT][hapmap]
rs6829144	0.81[ASN][1000 genomes]
rs6829716	0.87[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6830848	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs6836632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6843340	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6848073	0.86[JPT][hapmap]
rs6855022	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6856448	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7438704	0.85[JPT][hapmap]
rs7654770	0.87[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7661515	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7667288	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7670939	0.81[EUR][1000 genomes]
rs7678379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7679210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7683398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7693461	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7697851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs776584	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs776590	0.87[EUR][1000 genomes]
rs776591	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs776601	0.86[EUR][1000 genomes]
rs796555	0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs937888	0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs937889	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs952289	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9884546	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs992423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[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	nsv470034	chr4:48427773-48605628	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv594121	chr4:48427773-48605628	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10031777	OCIAD2	cis	cerebellum	SCAN
rs10031777	SLC10A4	cis	lung	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48487200-48505800	Weak transcription	A549	lung
2	chr4:48492400-48500800	Weak transcription	Brain Substantia Nigra	brain
3	chr4:48492600-48510600	Weak transcription	HepG2	liver
4	chr4:48492800-48500200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr4:48492800-48500800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:48493600-48500800	Weak transcription	Left Ventricle	heart
7	chr4:48493600-48509200	Weak transcription	Pancreas	Pancrea
8	chr4:48493600-48510600	Weak transcription	Gastric	stomach
9	chr4:48493600-48523000	Weak transcription	Right Ventricle	heart
10	chr4:48493800-48499600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:48493800-48500800	Weak transcription	Ovary	ovary
12	chr4:48493800-48502800	Weak transcription	Spleen	Spleen
13	chr4:48493800-48509600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr4:48493800-48510600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:48494000-48499000	Weak transcription	Placenta	Placenta
16	chr4:48494000-48511600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr4:48494000-48511800	Weak transcription	Colon Smooth Muscle	Colon
18	chr4:48494200-48499800	Weak transcription	Adipose Nuclei	Adipose
19	chr4:48494200-48499800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:48494200-48500200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr4:48494200-48500800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:48494200-48509800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:48494200-48510600	Weak transcription	HSMMtube	muscle
24	chr4:48494400-48498600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr4:48494600-48499800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr4:48494600-48500400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:48494600-48501000	Weak transcription	Brain Anterior Caudate	brain
28	chr4:48494800-48499400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:48494800-48500200	Weak transcription	GM12878-XiMat	blood
30	chr4:48494800-48500800	Weak transcription	Brain Angular Gyrus	brain
31	chr4:48494800-48509400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr4:48494800-48510600	Weak transcription	Esophagus	oesophagus
33	chr4:48495000-48499600	Weak transcription	Primary T cells from cord blood	blood
34	chr4:48495000-48499800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:48495000-48499800	Weak transcription	Brain Hippocampus Middle	brain
36	chr4:48495000-48499800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:48495000-48501400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr4:48495000-48510000	Weak transcription	Brain Germinal Matrix	brain
39	chr4:48495200-48500000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:48495200-48500000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr4:48495200-48500200	Weak transcription	Liver	Liver
42	chr4:48495200-48500200	Weak transcription	HMEC	breast
43	chr4:48495200-48500800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr4:48495200-48501000	Weak transcription	NH-A	brain
45	chr4:48495200-48502800	Weak transcription	Thymus	Thymus
46	chr4:48495200-48513600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr4:48495400-48501000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr4:48495400-48523000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr4:48495600-48499600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr4:48495600-48500400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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