Variant report

Variant	rs617834
Chromosome Location	chr8:61519325-61519326
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 130 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10096140	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10098769	0.92[CEU][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10102740	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10106752	1.00[YRI][hapmap]
rs1017861	1.00[YRI][hapmap]
rs1017862	1.00[YRI][hapmap]
rs10435601	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10808709	0.89[CEU][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10808710	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10957142	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10957144	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10957145	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10957147	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10957150	0.92[CEU][hapmap]
rs10957151	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1120591	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11774081	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11776939	0.82[EUR][1000 genomes]
rs11777673	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11777706	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11995549	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11996592	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12678742	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12680437	1.00[YRI][hapmap]
rs12680781	0.90[EUR][1000 genomes]
rs12681129	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1319104	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1319105	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13257359	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13262390	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13265543	0.88[EUR][1000 genomes]
rs13276831	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13439252	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1552071	0.81[EUR][1000 genomes]
rs17814894	0.81[EUR][1000 genomes]
rs1842389	0.82[EUR][1000 genomes]
rs1893272	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1941463	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2013112	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2056415	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2096890	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2155829	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2186986	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2272620	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2272621	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2326560	0.93[CEU][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2326561	0.93[CEU][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2326562	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2326568	0.93[CEU][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2326569	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2326570	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2326571	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2625441	0.93[CEU][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2625446	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2680297	1.00[YRI][hapmap]
rs28649594	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2875967	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2875968	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2875973	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2875974	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2930040	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2946154	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2981277	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3735825	0.92[CEU][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3735826	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3929643	0.89[EUR][1000 genomes]
rs41420549	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4288413	1.00[YRI][hapmap]
rs4403445	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4452821	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4738813	1.00[YRI][hapmap]
rs4738816	1.00[YRI][hapmap]
rs4738817	1.00[YRI][hapmap]
rs55825491	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56294255	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs586377	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs595255	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600811	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs603035	0.93[CEU][hapmap]
rs608401	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs615031	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs625850	0.92[CEU][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs629268	0.92[CEU][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs631408	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6471885	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6471886	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6471888	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs652422	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659118	0.89[EUR][1000 genomes]
rs660865	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs669599	0.93[CEU][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs671204	1.00[YRI][hapmap]
rs67420552	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs684066	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs687978	0.93[CEU][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6984378	0.81[EUR][1000 genomes]
rs6987084	0.93[CEU][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6992869	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6993019	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6995515	0.89[CEU][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7000166	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7001696	0.88[EUR][1000 genomes]
rs7007434	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7012181	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7013249	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7413	0.92[CEU][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7815543	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7822169	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7822621	1.00[YRI][hapmap]
rs7824045	0.93[CEU][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7825612	0.82[EUR][1000 genomes]
rs7827453	0.93[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7829359	0.93[CEU][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7830710	0.81[EUR][1000 genomes]
rs7834395	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7839474	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7839516	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs7842586	0.93[CEU][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs876957	1.00[YRI][hapmap]
rs900503	1.00[YRI][hapmap]
rs900504	1.00[YRI][hapmap]
rs9298039	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs948422	0.88[EUR][1000 genomes]
rs9643523	0.93[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv530383	chr8:61431756-61605551	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv870164	chr8:61484657-61529482	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv6218	chr8:61485410-61530933	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1796952	chr8:61492893-61531418	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv831335	chr8:61497540-61688992	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs617834	RAB2A	cis	Thyroid	GTEx
rs617834	RAB2	cis	normal skin	skin_eQTL
rs617834	RP11-163N6.2	cis	Thyroid	GTEx
rs617834	RAB2A	cis	multi-tissue	Pritchard
rs617834	RAB2	cis	uninvolved skin	skin_eQTL
rs617834	RAB2	cis	lesional skin	skin_eQTL
rs617834	RAB2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61481000-61527400	Weak transcription	Psoas Muscle	Psoas
2	chr8:61500400-61542200	Weak transcription	Hela-S3	cervix
3	chr8:61506000-61523200	Weak transcription	Fetal Heart	heart
4	chr8:61506000-61532200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr8:61506400-61532400	Weak transcription	NHLF	lung
6	chr8:61508000-61521600	Weak transcription	NHEK	skin
7	chr8:61508800-61533000	Weak transcription	HUVEC	blood vessel
8	chr8:61512400-61519600	Strong transcription	Osteobl	bone
9	chr8:61512400-61526200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr8:61512600-61521800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr8:61512800-61522600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr8:61512800-61527800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr8:61513000-61519600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr8:61513000-61528400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr8:61513800-61519400	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr8:61515000-61519600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr8:61515200-61519400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr8:61515200-61519600	Strong transcription	Fetal Kidney	kidney
19	chr8:61515600-61521600	Weak transcription	Right Ventricle	heart
20	chr8:61515600-61532200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr8:61515600-61533400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr8:61516000-61532000	Weak transcription	NHDF-Ad	bronchial
23	chr8:61516200-61521400	Weak transcription	HMEC	breast
24	chr8:61516200-61533200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr8:61516800-61520400	Strong transcription	Liver	Liver
26	chr8:61517600-61520000	Strong transcription	Adipose Nuclei	Adipose
27	chr8:61517600-61520400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr8:61517800-61522200	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr8:61517800-61532200	Weak transcription	Small Intestine	intestine
30	chr8:61517800-61537800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr8:61518000-61521400	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr8:61518000-61521400	Weak transcription	HepG2	liver
33	chr8:61518000-61522800	Strong transcription	Fetal Lung	lung
34	chr8:61518000-61524000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr8:61518000-61524200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr8:61518000-61530800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr8:61518000-61532000	Weak transcription	Colon Smooth Muscle	Colon
38	chr8:61518000-61532000	Weak transcription	Fetal Brain Male	brain
39	chr8:61518000-61534000	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr8:61518000-61536600	Weak transcription	Aorta	Aorta
41	chr8:61518200-61519400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr8:61518200-61519600	Strong transcription	Fetal Intestine Large	intestine
43	chr8:61518200-61519600	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr8:61518200-61519800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr8:61518200-61520200	Weak transcription	Primary T cells from cord blood	blood
46	chr8:61518200-61520200	Strong transcription	Fetal Intestine Small	intestine
47	chr8:61518200-61520200	Weak transcription	Placenta	Placenta
48	chr8:61518200-61520200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr8:61518200-61520400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr8:61518200-61520400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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