Variant report

Variant	rs3779899
Chromosome Location	chr8:86058003-86058004
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10088120	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]
rs10090196	0.86[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs10091577	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10091710	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10100442	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10104630	0.90[JPT][hapmap]
rs1021583	0.95[JPT][hapmap]
rs11261468	0.80[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap]
rs11261471	0.90[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs12541445	0.90[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs12543256	0.95[JPT][hapmap]
rs12544332	0.86[JPT][hapmap]
rs12546106	0.95[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs12549421	0.87[ASN][1000 genomes]
rs12550160	0.95[JPT][hapmap]
rs12926	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1303806	0.81[JPT][hapmap]
rs13249364	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13259399	0.86[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs13269031	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13269739	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1390711	0.81[JPT][hapmap]
rs1496531	0.86[JPT][hapmap]
rs1496532	0.86[JPT][hapmap]
rs1553015	0.81[JPT][hapmap];0.92[MEX][hapmap]
rs16913600	0.86[CEU][hapmap];0.97[GIH][hapmap];0.84[TSI][hapmap]
rs16913681	0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs16913721	0.86[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs17740658	0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs1908762	0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs1995056	0.81[JPT][hapmap];0.91[MEX][hapmap]
rs1995057	0.90[JPT][hapmap]
rs1995058	0.81[JPT][hapmap]
rs2006767	0.86[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs2132589	0.95[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs2278459	0.90[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs2279701	0.90[JPT][hapmap]
rs2291786	0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs2291787	0.90[JPT][hapmap]
rs2403082	0.83[EUR][1000 genomes]
rs2403083	0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2403084	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2403085	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2403086	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2403088	1.00[CEU][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2403089	0.84[EUR][1000 genomes]
rs2403104	0.81[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs28621707	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2896452	0.90[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap]
rs2896454	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34103685	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34527380	0.92[ASN][1000 genomes]
rs3779901	0.95[JPT][hapmap]
rs3808538	0.86[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs3808539	0.81[JPT][hapmap]
rs4150859	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4150862	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4150865	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4150867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4150868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4150869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4150884	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4150893	0.86[CEU][hapmap];0.81[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4150897	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4150909	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs4150942	0.86[CEU][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs4150944	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs4150964	0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs4150974	0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs4150977	0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs4609189	0.95[JPT][hapmap]
rs4739700	0.86[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap]
rs4740043	1.00[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4740044	0.86[JPT][hapmap]
rs4740045	0.95[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs4740049	0.81[JPT][hapmap];0.92[MEX][hapmap]
rs62527168	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62527173	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6605609	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6605610	0.95[JPT][hapmap]
rs6605611	0.95[JPT][hapmap]
rs6605624	0.90[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs6605625	0.84[EUR][1000 genomes]
rs6986704	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6990449	0.85[JPT][hapmap]
rs6993387	0.86[JPT][hapmap]
rs6994113	0.95[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs7001359	0.90[JPT][hapmap]
rs7004765	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7008032	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7008772	0.86[JPT][hapmap]
rs7010228	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7011926	0.81[JPT][hapmap];0.92[MEX][hapmap]
rs7015758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7814435	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7818090	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7818163	0.86[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap]
rs7823218	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7826589	0.85[JPT][hapmap]
rs7827175	0.95[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs7829050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7829144	0.80[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap]
rs7841142	0.80[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap]
rs7842013	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs903895	0.81[JPT][hapmap]
rs903896	0.81[JPT][hapmap];0.92[MEX][hapmap]
rs903897	0.81[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs3779899	LRRCC1	cis	parietal	SCAN
rs3779899	LRRCC1	cis	lesional skin	skin_eQTL
rs3779899	C8orf59	cis	cerebellum	SCAN
rs3779899	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs3779899	CA13	cis	cerebellum	SCAN
rs3779899	C8orf59	cis	parietal	SCAN
rs3779899	LRRCC1	cis	Esophagus Mucosa	GTEx
rs3779899	LRRCC1	cis	Artery Tibial	GTEx
rs3779899	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs3779899	ENSG00000133739	cis	multi-tissue	Pritchard
rs3779899	LRRCC1	cis	uninvolved skin	skin_eQTL
rs3779899	LRRCC1	cis	cerebellum	SCAN
rs3779899	LRRCC1	cis	normal skin	skin_eQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86020400-86062600	Weak transcription	Pancreas	Pancrea
2	chr8:86020600-86058800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr8:86021200-86058800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr8:86021200-86059600	Weak transcription	Fetal Brain Male	brain
5	chr8:86021400-86058400	Weak transcription	Brain Germinal Matrix	brain
6	chr8:86028400-86059000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr8:86033000-86059800	Weak transcription	Fetal Thymus	thymus
8	chr8:86037000-86061200	Weak transcription	Brain Anterior Caudate	brain
9	chr8:86039600-86058400	Weak transcription	Esophagus	oesophagus
10	chr8:86040600-86062000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr8:86043000-86058800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr8:86044200-86060000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr8:86046600-86064800	Weak transcription	Thymus	Thymus
14	chr8:86046600-86065800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr8:86048800-86059000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr8:86049400-86065800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr8:86050800-86061400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr8:86051000-86059800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr8:86054200-86059800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr8:86055000-86059800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr8:86055000-86062400	Weak transcription	Dnd41	blood
22	chr8:86055600-86058400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr8:86055800-86058200	Weak transcription	Fetal Stomach	stomach
24	chr8:86055800-86058400	Weak transcription	Lung	lung
25	chr8:86055800-86058800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr8:86055800-86059000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr8:86055800-86059200	Weak transcription	Fetal Intestine Small	intestine
28	chr8:86055800-86059600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr8:86056200-86058800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr8:86056400-86058200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr8:86056400-86058800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr8:86056600-86058600	Weak transcription	K562	blood
33	chr8:86057000-86059200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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