Variant report

Variant	rs4739700
Chromosome Location	chr8:86183670-86183671
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 135 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10088120	0.86[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs10090196	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.89[ASN][1000 genomes]
rs10095352	0.90[JPT][hapmap]
rs10100442	0.83[TSI][hapmap]
rs1014303	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1021583	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10907474	0.86[JPT][hapmap]
rs11261468	0.95[JPT][hapmap];0.96[MEX][hapmap]
rs11261471	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap]
rs11261472	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11261474	0.91[JPT][hapmap]
rs11985733	0.91[JPT][hapmap]
rs11989660	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12114575	0.88[ASN][1000 genomes]
rs12541445	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap]
rs12543256	0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs12544332	0.81[JPT][hapmap]
rs12546106	0.83[CHB][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs12550160	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs1303806	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1303807	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13252971	0.90[JPT][hapmap]
rs13259399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13269739	0.86[JPT][hapmap]
rs1390711	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1493302	0.91[JPT][hapmap]
rs1496529	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1496530	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs1496531	0.81[JPT][hapmap]
rs1496532	0.81[JPT][hapmap]
rs1532423	0.86[JPT][hapmap]
rs1532424	0.91[JPT][hapmap]
rs1553015	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16913681	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs16913721	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17042	0.86[JPT][hapmap]
rs17740658	0.83[CHB][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs1845891	0.80[ASN][1000 genomes]
rs1845892	0.80[ASN][1000 genomes]
rs1908762	0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.80[ASN][1000 genomes]
rs1995056	0.95[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1995057	0.86[JPT][hapmap]
rs1995058	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2006767	0.87[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.82[ASN][1000 genomes]
rs2055077	0.86[JPT][hapmap]
rs20571	0.91[JPT][hapmap]
rs2072696	0.90[JPT][hapmap]
rs2132589	0.83[CHB][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs2278459	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2279701	0.86[JPT][hapmap]
rs2291786	0.83[CHB][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs2291787	0.86[JPT][hapmap]
rs2403083	0.86[JPT][hapmap]
rs2403085	0.86[JPT][hapmap]
rs2403086	0.86[JPT][hapmap]
rs2403088	0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs2403104	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2548281	0.86[JPT][hapmap]
rs2645049	0.86[JPT][hapmap]
rs28439950	0.80[ASN][1000 genomes]
rs28677919	0.89[ASN][1000 genomes]
rs2896452	0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes]
rs2896453	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2896454	0.86[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs3087782	0.86[JPT][hapmap]
rs34103685	0.86[JPT][hapmap];0.84[MEX][hapmap]
rs35285802	0.82[ASN][1000 genomes]
rs3758076	0.91[JPT][hapmap]
rs3779899	0.86[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap]
rs3779901	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs3808538	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3808539	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3808540	0.91[CEU][hapmap];0.82[GIH][hapmap];0.84[EUR][1000 genomes]
rs4150867	0.86[JPT][hapmap]
rs4150868	0.86[JPT][hapmap]
rs4150869	0.85[JPT][hapmap]
rs4150893	0.86[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs4150909	0.86[JPT][hapmap]
rs4150942	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs4150944	0.86[JPT][hapmap]
rs4150964	0.83[CHB][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs4150974	0.83[CHB][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs4150977	0.83[CHB][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs4566	0.91[JPT][hapmap]
rs4609189	0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs4617148	0.80[ASN][1000 genomes]
rs4739698	0.80[ASN][1000 genomes]
rs4739702	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4740043	0.91[JPT][hapmap]
rs4740044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4740045	0.83[CHB][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs4740047	0.80[ASN][1000 genomes]
rs4740048	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4740049	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62527225	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6605610	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs6605611	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs6605624	0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap]
rs67573812	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6987641	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6988475	0.90[JPT][hapmap]
rs6990449	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6990452	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6993316	0.80[ASN][1000 genomes]
rs6993387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6994113	0.83[CHB][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs6997458	0.86[JPT][hapmap]
rs7001359	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7004871	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7008772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7011926	0.95[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7015758	0.86[JPT][hapmap]
rs7016369	0.86[JPT][hapmap]
rs725605	0.81[JPT][hapmap]
rs7818163	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];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7826589	0.91[JPT][hapmap]
rs7827175	0.83[CHB][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs7829050	0.86[JPT][hapmap]
rs7829144	0.95[JPT][hapmap];0.96[MEX][hapmap]
rs7833737	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7835303	0.88[ASN][1000 genomes]
rs7835882	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7837275	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7839129	0.82[ASN][1000 genomes]
rs7841142	0.95[JPT][hapmap];0.96[MEX][hapmap]
rs903895	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs903896	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs903897	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs931505	0.86[JPT][hapmap]
rs9969643	0.91[JPT][hapmap]
rs9987281	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018483	chr8:86142258-86547831	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024759	chr8:86162507-86361533	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv539659	chr8:86162507-86361533	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv981998	chr8:86183119-86187966	Weak transcription Enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4739700	CA13	cis	Lymphoblastoid	GTEx
rs4739700	C8orf59	cis	lymphoblastoid	seeQTL
rs4739700	C8orf59	cis	parietal	SCAN
rs4739700	LRRCC1	cis	cerebellum	SCAN
rs4739700	C8orf59	cis	cerebellum	SCAN
rs4739700	CA13	cis	lymphoblastoid	seeQTL
rs4739700	LRRCC1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86158400-86185800	Weak transcription	Lung	lung
2	chr8:86158400-86188200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr8:86158400-86188200	Weak transcription	Esophagus	oesophagus
4	chr8:86158400-86191400	Weak transcription	Pancreas	Pancrea
5	chr8:86158800-86185600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr8:86158800-86185800	Weak transcription	Fetal Stomach	stomach
7	chr8:86158800-86186800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr8:86158800-86189600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr8:86158800-86191400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr8:86167800-86185600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr8:86168000-86187800	Weak transcription	HMEC	breast
12	chr8:86168000-86196200	Weak transcription	NHEK	skin
13	chr8:86168000-86199000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr8:86170600-86191800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr8:86170800-86204400	Weak transcription	Ovary	ovary
16	chr8:86172200-86191400	Weak transcription	Primary T cells from cord blood	blood
17	chr8:86174600-86198200	Weak transcription	Left Ventricle	heart
18	chr8:86175800-86191200	Weak transcription	Brain Hippocampus Middle	brain
19	chr8:86175800-86191800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr8:86176400-86195000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr8:86176800-86187800	Weak transcription	Primary B cells from cord blood	blood
22	chr8:86177200-86187600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr8:86177600-86191200	Weak transcription	Right Ventricle	heart
24	chr8:86178000-86198200	Weak transcription	Aorta	Aorta
25	chr8:86178200-86184200	Weak transcription	Brain Angular Gyrus	brain
26	chr8:86178200-86193400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr8:86178600-86185600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr8:86179000-86191200	Weak transcription	Stomach Mucosa	stomach
29	chr8:86179800-86185800	Weak transcription	Gastric	stomach
30	chr8:86180000-86185400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr8:86180000-86187200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr8:86180200-86184200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr8:86181200-86191400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr8:86181600-86190800	Weak transcription	Small Intestine	intestine
35	chr8:86181600-86191400	Weak transcription	Fetal Lung	lung
36	chr8:86182000-86183800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr8:86182000-86184800	Strong transcription	Duodenum Mucosa	Duodenum
38	chr8:86182200-86189200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr8:86182400-86189200	Weak transcription	Liver	Liver
40	chr8:86182600-86184000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr8:86182600-86184000	Weak transcription	Fetal Intestine Large	intestine
42	chr8:86182600-86184000	Weak transcription	Fetal Intestine Small	intestine
43	chr8:86182600-86185200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr8:86182600-86185200	Weak transcription	HepG2	liver
45	chr8:86182600-86196000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr8:86182800-86183800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr8:86182800-86185800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr8:86183000-86190000	Weak transcription	Colonic Mucosa	Colon

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