Variant report

Variant	rs13119041
Chromosome Location	chr4:48645230-48645231
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10003273	0.85[AMR][1000 genomes]
rs10008265	0.85[AMR][1000 genomes]
rs10018344	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10029732	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10030853	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10031777	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10049761	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10938534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10938537	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11727343	0.92[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap]
rs11728565	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734019	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11737677	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11933919	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11945562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs12503599	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12506098	0.80[ASN][1000 genomes]
rs12645501	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs13108474	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13113370	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13119504	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13127730	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13138269	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13142540	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs13149083	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap]
rs13151534	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1507862	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1507865	0.87[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1517674	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1554256	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes]
rs1554258	0.85[AMR][1000 genomes]
rs1589107	0.83[AMR][1000 genomes]
rs1702798	0.83[EUR][1000 genomes]
rs1712767	0.85[EUR][1000 genomes]
rs1712768	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1712772	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17575720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17656040	0.80[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs17656076	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17656094	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs1876469	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2089503	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2102397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs2176460	0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2292231	0.85[AMR][1000 genomes]
rs2354312	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2354348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28470767	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];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28733443	0.83[EUR][1000 genomes]
rs2940324	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3107022	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34558821	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34635008	0.81[EUR][1000 genomes]
rs4536901	0.87[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs4695391	0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4695407	0.86[CHB][hapmap];0.92[YRI][hapmap]
rs59686413	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6447645	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6447647	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6447651	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6811148	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs6814811	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6818954	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6819159	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6829716	0.87[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap]
rs6830848	0.87[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs6836632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes]
rs6843340	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6855022	0.80[EUR][1000 genomes]
rs6856448	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7654032	0.88[CEU][hapmap];0.82[CHB][hapmap];0.88[YRI][hapmap]
rs7654770	0.87[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap]
rs7657332	1.00[JPT][hapmap];0.84[TSI][hapmap]
rs7657698	1.00[JPT][hapmap]
rs7660206	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs7661515	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7667288	0.88[ASW][hapmap];0.96[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];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7670939	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7678379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7679210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7682859	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7683398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7693461	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7697522	1.00[JPT][hapmap]
rs7697851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs776584	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs776588	0.81[EUR][1000 genomes]
rs776590	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs776591	0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs776601	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs796555	0.87[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs937888	0.87[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs937889	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs952289	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9884546	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs992423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs9997920	0.86[CHB][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13119041	SLC10A4	cis	lung	GTEx
rs13119041	OCIAD2	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48621200-48729400	Weak transcription	Thymus	Thymus
2	chr4:48621800-48655800	Weak transcription	Colonic Mucosa	Colon
3	chr4:48622800-48648400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:48627200-48652400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:48627200-48656400	Weak transcription	Fetal Intestine Small	intestine
6	chr4:48635200-48654000	Weak transcription	Fetal Intestine Large	intestine
7	chr4:48635200-48655000	Weak transcription	Dnd41	blood
8	chr4:48637600-48656400	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:48637800-48652400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:48637800-48653400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:48637800-48664200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:48638000-48647200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:48638000-48651600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr4:48638000-48653800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:48638000-48655400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:48638000-48655600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:48638000-48657200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr4:48638000-48663000	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr4:48638000-48664600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr4:48638400-48686200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr4:48638600-48652400	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr4:48638600-48655400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:48638600-48666000	Weak transcription	Primary B cells from cord blood	blood
24	chr4:48639400-48653400	Weak transcription	HMEC	breast
25	chr4:48639600-48647400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:48639600-48652200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr4:48641600-48645400	Enhancers	Brain Cingulate Gyrus	brain
28	chr4:48642000-48645600	Enhancers	Adipose Nuclei	Adipose
29	chr4:48642200-48647200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:48642200-48654800	Weak transcription	Stomach Mucosa	stomach
31	chr4:48642400-48645600	Enhancers	Fetal Heart	heart
32	chr4:48642400-48647400	Weak transcription	NHEK	skin
33	chr4:48643000-48647200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:48643000-48655200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:48643200-48645400	Enhancers	HUVEC	blood vessel
36	chr4:48643200-48647400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr4:48643200-48655600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr4:48643400-48652400	Weak transcription	Primary T cells from cord blood	blood
39	chr4:48644000-48645400	Enhancers	Fetal Lung	lung
40	chr4:48644000-48655600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr4:48644200-48645400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr4:48644400-48645400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr4:48644400-48645400	Enhancers	Muscle Satellite Cultured Cells	--
44	chr4:48644400-48645400	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr4:48644400-48645400	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr4:48644400-48645600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:48644600-48645400	Enhancers	Colon Smooth Muscle	Colon
48	chr4:48644600-48645400	Enhancers	Stomach Smooth Muscle	stomach
49	chr4:48644600-48645600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:48644800-48645400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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