Variant report

Variant	rs668139
Chromosome Location	chr5:68489836-68489837
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	chr5:68487593..68492001-chr5:68493438..68496143,4	K562	blood:
2	chr5:68400690..68402320-chr5:68488616..68490544,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10805428	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1134774	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11739602	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11741775	0.82[ASN][1000 genomes]
rs11741826	0.82[ASN][1000 genomes]
rs11742878	0.81[ASN][1000 genomes]
rs11745537	0.81[ASN][1000 genomes]
rs11745591	0.81[ASN][1000 genomes]
rs11951414	1.00[JPT][hapmap]
rs11952883	1.00[JPT][hapmap]
rs12188270	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12520485	0.84[EUR][1000 genomes]
rs13161541	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13163459	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13178023	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13182409	0.88[AMR][1000 genomes]
rs1976101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2054974	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2054975	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2054976	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2130756	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2172055	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2327638	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2327639	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28499200	0.81[ASN][1000 genomes]
rs2932785	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2932787	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2932788	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2932789	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2932790	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2932793	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2972357	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2972364	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972367	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972369	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972379	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972384	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972385	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34261117	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34449359	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34591347	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34657177	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs350092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs350096	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350118	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs350121	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4423955	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62373182	0.81[ASN][1000 genomes]
rs6865178	0.84[EUR][1000 genomes]
rs71622283	0.91[ASN][1000 genomes]
rs72767881	0.81[ASN][1000 genomes]
rs7706902	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7711657	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[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	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3378789	chr5:68438275-68540725	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv3445512	chr5:68472245-68495835	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs668139	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs668139	RAD17	cis	Muscle Skeletal	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68485800-68493800	Weak transcription	Lung	lung
2	chr5:68486000-68498200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:68486000-68498600	Weak transcription	Left Ventricle	heart
4	chr5:68486000-68505800	Weak transcription	Ovary	ovary
5	chr5:68486000-68513600	Weak transcription	Gastric	stomach
6	chr5:68486200-68490000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:68486200-68490000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:68486200-68490000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr5:68486200-68490200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr5:68486200-68490200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr5:68486200-68490200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:68486200-68491200	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr5:68486200-68492000	Weak transcription	Fetal Brain Female	brain
14	chr5:68486200-68492200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr5:68486200-68494200	Weak transcription	Fetal Lung	lung
16	chr5:68486200-68494400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr5:68486200-68494600	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr5:68486200-68494800	Weak transcription	Brain Substantia Nigra	brain
19	chr5:68486200-68496200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr5:68486200-68496200	Weak transcription	Brain Hippocampus Middle	brain
21	chr5:68486200-68497000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:68486200-68497600	Weak transcription	Fetal Heart	heart
23	chr5:68486200-68497600	Weak transcription	Pancreas	Pancrea
24	chr5:68486200-68498200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr5:68486200-68498400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr5:68486200-68499200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr5:68486200-68499400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr5:68486200-68500200	Weak transcription	Thymus	Thymus
29	chr5:68486200-68502000	Weak transcription	Placenta	Placenta
30	chr5:68486200-68502200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:68486200-68502600	Weak transcription	Small Intestine	intestine
32	chr5:68486200-68505200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr5:68486200-68509400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr5:68486200-68509400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:68486200-68509400	Weak transcription	HSMM	muscle
36	chr5:68486200-68512800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr5:68486400-68490000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr5:68486400-68491200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr5:68486400-68491800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr5:68486400-68491800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:68486400-68494400	Weak transcription	HMEC	breast
42	chr5:68486400-68494400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr5:68486400-68494600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr5:68486400-68494800	Weak transcription	Adipose Nuclei	Adipose
45	chr5:68486400-68496400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr5:68486400-68496800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr5:68486400-68502400	Weak transcription	NH-A	brain
48	chr5:68486400-68502600	Weak transcription	Fetal Kidney	kidney
49	chr5:68486400-68502600	Weak transcription	HUVEC	blood vessel
50	chr5:68486400-68512400	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links