Variant report

Variant	rs10088120
Chromosome Location	chr8:86052243-86052244
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10090196	0.86[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs10091577	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10091710	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10100442	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10104630	0.90[JPT][hapmap]
rs1021583	0.95[JPT][hapmap]
rs11261468	0.80[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs11261471	0.91[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs12541445	0.91[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs12543256	0.95[JPT][hapmap]
rs12546106	0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap]
rs12549421	0.91[ASN][1000 genomes]
rs12550160	0.95[JPT][hapmap]
rs12926	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1303806	0.82[JPT][hapmap]
rs13249364	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13259399	0.86[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs13269031	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13269739	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1390711	0.82[JPT][hapmap]
rs1553015	0.82[JPT][hapmap];0.88[MEX][hapmap]
rs16913600	0.82[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs16913681	0.95[JPT][hapmap]
rs16913721	0.86[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap]
rs17740658	0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap]
rs1908762	0.90[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap]
rs1995056	0.87[MEX][hapmap]
rs1995057	0.91[JPT][hapmap]
rs1995058	0.82[JPT][hapmap]
rs2006767	0.86[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap]
rs2132589	0.95[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs2278459	0.91[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap]
rs2279701	0.91[JPT][hapmap]
rs2291786	0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap]
rs2291787	0.91[JPT][hapmap]
rs2403082	0.81[EUR][1000 genomes]
rs2403083	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2403084	0.83[EUR][1000 genomes]
rs2403085	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2403086	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2403088	1.00[CEU][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2403089	0.82[EUR][1000 genomes]
rs2403104	0.82[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs28621707	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2896452	0.91[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs2896454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34103685	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34527380	0.93[ASN][1000 genomes]
rs3779899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3779901	0.95[JPT][hapmap]
rs3808538	0.86[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs3808539	0.82[JPT][hapmap]
rs4150859	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4150862	0.90[EUR][1000 genomes]
rs4150865	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4150867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4150868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4150869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4150884	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4150893	0.86[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs4150897	0.83[EUR][1000 genomes]
rs4150909	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs4150942	0.86[CEU][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs4150944	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4150964	0.95[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap]
rs4150974	0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs4150977	0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs4609189	0.95[JPT][hapmap]
rs4739700	0.86[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs4740043	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4740044	0.86[JPT][hapmap]
rs4740045	0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap]
rs4740049	0.82[JPT][hapmap];0.88[MEX][hapmap]
rs62527168	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62527173	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6605609	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6605610	0.95[JPT][hapmap]
rs6605611	0.95[JPT][hapmap]
rs6605624	0.90[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6605625	0.82[EUR][1000 genomes]
rs6986704	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6990449	0.86[JPT][hapmap]
rs6993387	0.86[JPT][hapmap]
rs6994113	0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap]
rs7001359	0.91[JPT][hapmap]
rs7004765	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7008032	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7008772	0.86[JPT][hapmap]
rs7010228	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7011926	0.82[JPT][hapmap];0.88[MEX][hapmap]
rs7015758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7814435	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7818090	0.87[EUR][1000 genomes]
rs7818163	0.86[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs7823218	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7826589	0.85[JPT][hapmap]
rs7827175	0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap]
rs7829050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7829144	0.80[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap]
rs7841142	0.80[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap]
rs7842013	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs903895	0.82[JPT][hapmap]
rs903896	0.82[JPT][hapmap];0.88[MEX][hapmap]
rs903897	0.82[JPT][hapmap]
rs9692962	0.90[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	esv3481417	chr8:85279453-86145229	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3481418	chr8:85279453-86145229	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv1797206	chr8:86023237-86060072	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	esv1800945	chr8:86030101-86060072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10088120	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs10088120	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs10088120	C8orf59	cis	parietal	SCAN
rs10088120	LRRCC1	cis	lesional skin	skin_eQTL
rs10088120	LRRCC1	cis	normal skin	skin_eQTL
rs10088120	LRRCC1	cis	uninvolved skin	skin_eQTL
rs10088120	CA13	cis	cerebellum	SCAN
rs10088120	C8orf59	cis	cerebellum	SCAN
rs10088120	LRRCC1	cis	Artery Tibial	GTEx
rs10088120	LRRCC1	cis	cerebellum	SCAN
rs10088120	LRRCC1	cis	parietal	SCAN
rs10088120	LRRCC1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86020000-86057400	Weak transcription	Small Intestine	intestine
2	chr8:86020400-86054800	Weak transcription	Lung	lung
3	chr8:86020400-86055400	Weak transcription	Fetal Kidney	kidney
4	chr8:86020400-86055400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr8:86020400-86056400	Weak transcription	Gastric	stomach
6	chr8:86020400-86057400	Weak transcription	Aorta	Aorta
7	chr8:86020400-86062600	Weak transcription	Pancreas	Pancrea
8	chr8:86020600-86052400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr8:86020600-86054600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr8:86020600-86058800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr8:86021200-86053600	Weak transcription	Brain Substantia Nigra	brain
12	chr8:86021200-86058800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr8:86021200-86059600	Weak transcription	Fetal Brain Male	brain
14	chr8:86021400-86058400	Weak transcription	Brain Germinal Matrix	brain
15	chr8:86025200-86057400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr8:86028400-86059000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr8:86028600-86056400	Weak transcription	Ovary	ovary
18	chr8:86032800-86057400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr8:86033000-86059800	Weak transcription	Fetal Thymus	thymus
20	chr8:86035200-86055600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr8:86037000-86061200	Weak transcription	Brain Anterior Caudate	brain
22	chr8:86037400-86056000	Weak transcription	Right Ventricle	heart
23	chr8:86038000-86057200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr8:86038800-86057400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr8:86039400-86056200	Weak transcription	Brain Hippocampus Middle	brain
26	chr8:86039600-86058400	Weak transcription	Esophagus	oesophagus
27	chr8:86040200-86056600	Weak transcription	Fetal Brain Female	brain
28	chr8:86040600-86052400	Weak transcription	NHDF-Ad	bronchial
29	chr8:86040600-86062000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr8:86042200-86052400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr8:86043000-86058800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr8:86043200-86053000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr8:86043200-86057200	Weak transcription	Left Ventricle	heart
34	chr8:86044200-86060000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr8:86044400-86056200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr8:86045600-86056400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr8:86045600-86057200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr8:86046200-86053400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr8:86046200-86055600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr8:86046600-86055000	Weak transcription	Colon Smooth Muscle	Colon
41	chr8:86046600-86064800	Weak transcription	Thymus	Thymus
42	chr8:86046600-86065800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr8:86047400-86052600	Weak transcription	Placenta	Placenta
44	chr8:86048800-86054200	Weak transcription	Fetal Stomach	stomach
45	chr8:86048800-86059000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr8:86049000-86055000	Strong transcription	Dnd41	blood
47	chr8:86049400-86053400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr8:86049400-86053800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr8:86049400-86054200	Weak transcription	Fetal Intestine Small	intestine
50	chr8:86049400-86056200	Weak transcription	Placenta Amnion	Placenta Amnion

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