Variant report

Variant	rs12543256
Chromosome Location	chr8:86187426-86187427
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:86176950..86178514-chr8:86185372..86187866,2	K562	blood:

Extended variants
information (count: 135 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10088120	0.95[JPT][hapmap]
rs10090196	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10091582	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10095352	0.82[JPT][hapmap]
rs10099251	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10100442	0.89[JPT][hapmap]
rs10106970	0.90[ASN][1000 genomes]
rs10107686	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10110461	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10111971	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1021583	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11261468	0.85[JPT][hapmap]
rs11261469	0.96[ASN][1000 genomes]
rs11261471	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11261474	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11985733	0.82[JPT][hapmap]
rs12114575	0.89[EUR][1000 genomes]
rs12541299	0.90[ASN][1000 genomes]
rs12541445	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12544332	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs12546106	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12550160	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12679400	0.90[ASN][1000 genomes]
rs1303806	0.87[JPT][hapmap]
rs13252971	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs13259399	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs13259464	0.86[ASN][1000 genomes]
rs13269739	0.95[JPT][hapmap]
rs1390711	0.87[JPT][hapmap]
rs1493302	0.83[JPT][hapmap]
rs1496529	0.83[JPT][hapmap]
rs1496530	0.82[JPT][hapmap]
rs1496531	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1496532	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1496533	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1532424	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1553015	0.86[JPT][hapmap]
rs1553016	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1553017	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16913681	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16913721	0.83[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs17740658	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1809819	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1845891	0.97[ASN][1000 genomes]
rs1845892	0.97[ASN][1000 genomes]
rs1908762	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1995056	0.81[JPT][hapmap]
rs1995057	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes]
rs1995058	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs2006767	0.95[CHB][hapmap];0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs20571	0.82[JPT][hapmap]
rs2072696	0.82[JPT][hapmap]
rs2132589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2132590	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2278459	0.85[JPT][hapmap]
rs2279700	0.90[ASN][1000 genomes]
rs2279701	0.96[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2291786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2291787	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2403083	0.92[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2403084	0.83[ASN][1000 genomes]
rs2403085	0.92[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2403086	0.92[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2403088	0.85[JPT][hapmap]
rs2403104	0.86[JPT][hapmap]
rs28374336	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28377260	0.88[ASN][1000 genomes]
rs28439950	0.97[ASN][1000 genomes]
rs28564613	0.92[ASN][1000 genomes]
rs2896452	0.85[JPT][hapmap]
rs2896454	0.95[JPT][hapmap]
rs34103685	0.95[JPT][hapmap]
rs35558766	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3758076	0.83[JPT][hapmap]
rs3779899	0.95[JPT][hapmap]
rs3779901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3808538	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs3808539	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs4150867	0.95[JPT][hapmap]
rs4150868	0.95[JPT][hapmap]
rs4150869	0.90[JPT][hapmap]
rs4150893	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4150897	0.82[ASN][1000 genomes]
rs4150909	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4150942	0.85[JPT][hapmap]
rs4150944	0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4150962	0.88[ASN][1000 genomes]
rs4150964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4150974	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4150977	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4566	0.82[JPT][hapmap]
rs4609189	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4617148	0.97[ASN][1000 genomes]
rs4739698	0.97[ASN][1000 genomes]
rs4739700	0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs4740043	0.81[JPT][hapmap]
rs4740044	0.91[JPT][hapmap]
rs4740045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4740047	0.97[ASN][1000 genomes]
rs4740049	0.86[JPT][hapmap]
rs6605610	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6605611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6605613	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6605624	0.85[JPT][hapmap]
rs6988475	0.82[JPT][hapmap]
rs6990449	0.93[JPT][hapmap]
rs6993316	0.97[ASN][1000 genomes]
rs6993387	0.91[JPT][hapmap]
rs6994113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7001359	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7008772	0.91[JPT][hapmap]
rs7011001	0.92[ASN][1000 genomes]
rs7011926	0.86[JPT][hapmap]
rs7015758	0.95[JPT][hapmap]
rs7818163	0.83[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7821629	0.90[ASN][1000 genomes]
rs7826511	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7826589	0.81[JPT][hapmap]
rs7827175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7829050	0.95[JPT][hapmap]
rs7829144	0.85[JPT][hapmap]
rs7829240	0.90[ASN][1000 genomes]
rs7835303	0.89[EUR][1000 genomes]
rs7839129	0.99[ASN][1000 genomes]
rs7841142	0.85[JPT][hapmap]
rs903895	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs903896	0.86[JPT][hapmap]
rs903897	1.00[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs9329908	0.95[ASN][1000 genomes]
rs9969643	0.82[JPT][hapmap]
rs9987281	0.82[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12543256	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs12543256	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs12543256	CA13	cis	multi-tissue	Pritchard
rs12543256	LRRCC1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86158400-86188200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr8:86158400-86188200	Weak transcription	Esophagus	oesophagus
3	chr8:86158400-86191400	Weak transcription	Pancreas	Pancrea
4	chr8:86158800-86189600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr8:86158800-86191400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr8:86168000-86187800	Weak transcription	HMEC	breast
7	chr8:86168000-86196200	Weak transcription	NHEK	skin
8	chr8:86168000-86199000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr8:86170600-86191800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr8:86170800-86204400	Weak transcription	Ovary	ovary
11	chr8:86172200-86191400	Weak transcription	Primary T cells from cord blood	blood
12	chr8:86174600-86198200	Weak transcription	Left Ventricle	heart
13	chr8:86175800-86191200	Weak transcription	Brain Hippocampus Middle	brain
14	chr8:86175800-86191800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr8:86176400-86195000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr8:86176800-86187800	Weak transcription	Primary B cells from cord blood	blood
17	chr8:86177200-86187600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr8:86177600-86191200	Weak transcription	Right Ventricle	heart
19	chr8:86178000-86198200	Weak transcription	Aorta	Aorta
20	chr8:86178200-86193400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr8:86179000-86191200	Weak transcription	Stomach Mucosa	stomach
22	chr8:86181200-86191400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr8:86181600-86190800	Weak transcription	Small Intestine	intestine
24	chr8:86181600-86191400	Weak transcription	Fetal Lung	lung
25	chr8:86182200-86189200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr8:86182400-86189200	Weak transcription	Liver	Liver
27	chr8:86182600-86196000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr8:86183000-86190000	Weak transcription	Colonic Mucosa	Colon
29	chr8:86183800-86190200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr8:86183800-86190800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr8:86184000-86188000	Strong transcription	Fetal Intestine Large	intestine
32	chr8:86184000-86190400	Strong transcription	Fetal Intestine Small	intestine
33	chr8:86184200-86190200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr8:86184400-86187600	Weak transcription	Thymus	Thymus
35	chr8:86184400-86191200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr8:86185200-86187800	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr8:86185400-86190000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr8:86185600-86187800	Strong transcription	Duodenum Mucosa	Duodenum
39	chr8:86185600-86190200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr8:86185600-86190200	Weak transcription	HepG2	liver
41	chr8:86185800-86187800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr8:86186200-86188200	Weak transcription	Gastric	stomach
43	chr8:86186200-86191400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr8:86186400-86188200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr8:86186400-86188200	Weak transcription	Lung	lung
46	chr8:86186400-86190800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr8:86186400-86191400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr8:86186600-86198800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr8:86186800-86188800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr8:86187200-86187800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood

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