Variant report

Variant	rs13262390
Chromosome Location	chr8:61446683-61446684
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:61446080..61449984-chr8:61450187..61453162,6	K562	blood:
2	chr8:61445869..61450091-chr8:61450711..61454496,4	K562	blood:
3	chr8:61427036..61429414-chr8:61445945..61448319,2	K562	blood:

Variant related genes	Relation type
ENSG00000251396	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10096140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10098769	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10102740	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10435601	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10808709	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10808710	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10957142	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10957144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10957145	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10957147	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10957151	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1120591	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11774081	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11776939	0.83[EUR][1000 genomes]
rs11777673	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11777706	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11995549	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11996592	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12678742	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12680781	0.89[EUR][1000 genomes]
rs12681129	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1319104	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1319105	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13257359	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13265543	0.89[EUR][1000 genomes]
rs13276831	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13439252	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1552071	0.82[EUR][1000 genomes]
rs17814894	0.82[EUR][1000 genomes]
rs1842389	0.83[EUR][1000 genomes]
rs1893272	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1941463	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2013112	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2056415	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2096890	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2155829	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2186986	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2272620	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272621	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2326560	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2326561	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2326562	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2326568	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2326569	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2326570	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2326571	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2625441	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2625446	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28649594	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2875967	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2875968	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2875973	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2875974	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2930040	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2946154	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2981277	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3735825	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3735826	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3929643	0.90[EUR][1000 genomes]
rs41420549	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4403445	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4452821	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55825491	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56294255	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586377	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs595255	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs600811	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs608401	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs615031	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs617834	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs625850	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs629268	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs631408	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6471885	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6471886	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6471888	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs652422	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs659118	0.88[EUR][1000 genomes]
rs660865	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs669599	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67420552	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs684066	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs687978	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6984378	0.82[EUR][1000 genomes]
rs6987084	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6992869	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6993019	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6995515	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7000166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7001696	0.89[EUR][1000 genomes]
rs7007434	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7012181	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7013249	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7413	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7815543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7822169	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7824045	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7825612	0.83[EUR][1000 genomes]
rs7827453	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7829359	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7830710	0.82[EUR][1000 genomes]
rs7834395	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7839474	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7839516	0.89[EUR][1000 genomes]
rs7842586	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9298039	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs948422	0.89[EUR][1000 genomes]
rs9643523	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv972537	chr8:61443763-61449601	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13262390	RP11-163N6.2	cis	Thyroid	GTEx
rs13262390	RAB2A	Cis_1M	lymphoblastoid	RTeQTL
rs13262390	RAB2A	cis	Thyroid	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61431800-61446800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr8:61433800-61472600	Weak transcription	HUVEC	blood vessel
3	chr8:61434000-61447800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr8:61434600-61467600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr8:61434600-61472600	Weak transcription	Placenta	Placenta
6	chr8:61434800-61452200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr8:61434800-61458000	Weak transcription	Dnd41	blood
8	chr8:61434800-61480600	Weak transcription	HMEC	breast
9	chr8:61435400-61470800	Weak transcription	NHEK	skin
10	chr8:61435400-61471800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr8:61436800-61447000	Weak transcription	HepG2	liver
12	chr8:61437000-61450200	Weak transcription	Fetal Stomach	stomach
13	chr8:61437200-61462600	Weak transcription	NH-A	brain
14	chr8:61437400-61447000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr8:61437400-61463200	Weak transcription	HSMM	muscle
16	chr8:61437600-61446800	Weak transcription	NHDF-Ad	bronchial
17	chr8:61437600-61451000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr8:61437800-61446800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr8:61437800-61447000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr8:61438000-61446800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr8:61438000-61449800	Weak transcription	Aorta	Aorta
22	chr8:61438000-61488600	Weak transcription	Fetal Brain Female	brain
23	chr8:61438200-61450800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr8:61438400-61469600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr8:61439000-61453000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr8:61439400-61455800	Weak transcription	Fetal Thymus	thymus
27	chr8:61439400-61494600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr8:61439600-61448800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr8:61440000-61449800	Weak transcription	Esophagus	oesophagus
30	chr8:61440200-61450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr8:61440800-61446800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr8:61440800-61480000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr8:61441000-61446800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr8:61441400-61446800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr8:61442000-61447000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr8:61442200-61447200	Weak transcription	Fetal Lung	lung
37	chr8:61442600-61447400	Enhancers	Psoas Muscle	Psoas
38	chr8:61443200-61447400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr8:61443400-61446800	Weak transcription	Gastric	stomach
40	chr8:61443400-61446800	Weak transcription	K562	blood
41	chr8:61443800-61446800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr8:61443800-61446800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr8:61443800-61448200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr8:61443800-61472800	Weak transcription	Thymus	Thymus
45	chr8:61444000-61448000	Weak transcription	GM12878-XiMat	blood
46	chr8:61444000-61462800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr8:61444200-61448200	Weak transcription	Small Intestine	intestine
48	chr8:61444400-61448800	Enhancers	Right Ventricle	heart
49	chr8:61444600-61447000	Enhancers	Pancreas	Pancrea
50	chr8:61444600-61447200	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links