Variant report

Variant	rs7839129
Chromosome Location	chr8:86186224-86186225
allele	C/T
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: 78 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10090196	0.86[EUR][1000 genomes]
rs10091582	0.90[ASN][1000 genomes]
rs10099251	0.90[ASN][1000 genomes]
rs10106970	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10107686	0.84[ASN][1000 genomes]
rs10110461	0.89[ASN][1000 genomes]
rs10111971	0.90[ASN][1000 genomes]
rs1021583	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11261469	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11261471	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12541299	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12541445	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12543256	0.99[ASN][1000 genomes]
rs12546106	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12550160	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12679400	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13259464	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1496533	0.86[ASN][1000 genomes]
rs1553016	0.90[ASN][1000 genomes]
rs1553017	0.89[ASN][1000 genomes]
rs16913681	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16913721	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17740658	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1809819	0.86[ASN][1000 genomes]
rs1845891	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1845892	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1908762	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2006767	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132589	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2132590	0.98[ASN][1000 genomes]
rs2279700	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2279701	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291786	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2291787	0.84[ASN][1000 genomes]
rs2403083	0.84[ASN][1000 genomes]
rs2403084	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2403085	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2403086	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs28374336	0.90[ASN][1000 genomes]
rs28377260	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28439950	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28564613	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28677919	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35558766	0.89[ASN][1000 genomes]
rs3779901	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150893	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4150897	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4150909	0.82[ASN][1000 genomes]
rs4150944	0.84[ASN][1000 genomes]
rs4150962	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150964	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4150974	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4150977	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4609189	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4617148	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4739698	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4739700	0.82[ASN][1000 genomes]
rs4740045	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4740047	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6605610	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6605611	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6605613	0.89[ASN][1000 genomes]
rs6993316	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6993387	0.81[ASN][1000 genomes]
rs6994113	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7001359	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7004871	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7011001	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7818163	0.82[ASN][1000 genomes]
rs7821629	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7826511	0.82[ASN][1000 genomes]
rs7827175	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7829240	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9329908	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

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
rs7839129	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs7839129	LRRCC1	cis	Artery Tibial	GTEx
rs7839129	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs7839129	LRRCC1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:51 , 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	chr8:86158800-86186800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr8:86158800-86189600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr8:86158800-86191400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr8:86168000-86187800	Weak transcription	HMEC	breast
8	chr8:86168000-86196200	Weak transcription	NHEK	skin
9	chr8:86168000-86199000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr8:86170600-86191800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr8:86170800-86204400	Weak transcription	Ovary	ovary
12	chr8:86172200-86191400	Weak transcription	Primary T cells from cord blood	blood
13	chr8:86174600-86198200	Weak transcription	Left Ventricle	heart
14	chr8:86175800-86191200	Weak transcription	Brain Hippocampus Middle	brain
15	chr8:86175800-86191800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr8:86176400-86195000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr8:86176800-86187800	Weak transcription	Primary B cells from cord blood	blood
18	chr8:86177200-86187600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr8:86177600-86191200	Weak transcription	Right Ventricle	heart
20	chr8:86178000-86198200	Weak transcription	Aorta	Aorta
21	chr8:86178200-86193400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr8:86179000-86191200	Weak transcription	Stomach Mucosa	stomach
23	chr8:86180000-86187200	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr8:86181200-86191400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr8:86181600-86190800	Weak transcription	Small Intestine	intestine
26	chr8:86181600-86191400	Weak transcription	Fetal Lung	lung
27	chr8:86182200-86189200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr8:86182400-86189200	Weak transcription	Liver	Liver
29	chr8:86182600-86196000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr8:86183000-86190000	Weak transcription	Colonic Mucosa	Colon
31	chr8:86183800-86190200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr8:86183800-86190800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr8:86184000-86188000	Strong transcription	Fetal Intestine Large	intestine
34	chr8:86184000-86190400	Strong transcription	Fetal Intestine Small	intestine
35	chr8:86184200-86190200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr8:86184400-86187600	Weak transcription	Thymus	Thymus
37	chr8:86184400-86191200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr8:86185200-86187800	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr8:86185400-86190000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr8:86185600-86186400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr8:86185600-86186600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr8:86185600-86187800	Strong transcription	Duodenum Mucosa	Duodenum
43	chr8:86185600-86190200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr8:86185600-86190200	Weak transcription	HepG2	liver
45	chr8:86185800-86186400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr8:86185800-86186400	Strong transcription	Fetal Stomach	stomach
47	chr8:86185800-86186400	Strong transcription	Lung	lung
48	chr8:86185800-86187800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr8:86186000-86186400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr8:86186200-86188200	Weak transcription	Gastric	stomach

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