Variant report

Variant	rs10060234
Chromosome Location	chr5:40689996-40689997
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10056345	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064175	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1057631	0.81[CEU][hapmap]
rs1070446	0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap]
rs10737963	0.83[CEU][hapmap]
rs1097546	0.85[ASN][1000 genomes]
rs13354346	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13355305	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs154268	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs154275	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs154280	0.85[ASN][1000 genomes]
rs154284	0.85[ASN][1000 genomes]
rs1644962	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs171605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs192219	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs193864	0.83[ASN][1000 genomes]
rs193866	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2161521	0.85[ASN][1000 genomes]
rs249413	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs249414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249416	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249420	0.83[ASN][1000 genomes]
rs249422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs249423	0.85[ASN][1000 genomes]
rs249425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs249428	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs249429	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[ASN][1000 genomes]
rs257009	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs28569300	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs29740	0.85[ASN][1000 genomes]
rs29742	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs29743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs29744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs29761	0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap]
rs4133101	0.88[CEU][hapmap]
rs4277957	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4285273	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4315964	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4315965	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs432071	0.85[ASN][1000 genomes]
rs4345353	0.84[CEU][hapmap]
rs434778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4383756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4434423	0.82[CEU][hapmap];0.86[YRI][hapmap]
rs447810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs453037	0.85[ASN][1000 genomes]
rs4546432	0.87[CEU][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs4573034	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs457776	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs4607392	0.85[CEU][hapmap]
rs461404	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[ASN][1000 genomes]
rs466108	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs466962	0.83[ASN][1000 genomes]
rs4957344	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59069340	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59920139	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6451535	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6451537	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6871999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6896993	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7708680	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7711806	0.85[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap]
rs7726237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7737044	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs837101	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880539	chr5:40662257-40713645	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10060234		cis	Lymphoblastoid	GTEx
rs10060234	TTC33	Cis_1M	lymphoblastoid	RTeQTL
rs10060234	Hs.506072	cis	multi-tissue	Pritchard
rs10060234	RPL37	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40680800-40690800	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr5:40682400-40691400	Weak transcription	Spleen	Spleen
3	chr5:40682800-40691400	Weak transcription	Lung	lung
4	chr5:40683000-40691600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:40683000-40691600	Weak transcription	Esophagus	oesophagus
6	chr5:40683000-40692000	Weak transcription	Gastric	stomach
7	chr5:40683800-40690200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:40683800-40691600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr5:40684000-40690200	Weak transcription	Pancreas	Pancrea
10	chr5:40684000-40700600	Weak transcription	Left Ventricle	heart
11	chr5:40684600-40691600	Weak transcription	Fetal Stomach	stomach
12	chr5:40684600-40700400	Weak transcription	Right Ventricle	heart
13	chr5:40685400-40690400	Genic enhancers	Primary monocytes fromperipheralblood	blood
14	chr5:40685400-40691800	Weak transcription	Fetal Muscle Leg	muscle
15	chr5:40685400-40692000	Weak transcription	Aorta	Aorta
16	chr5:40685600-40690800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr5:40685800-40691600	Weak transcription	Colonic Mucosa	Colon
18	chr5:40686400-40690200	Weak transcription	Fetal Intestine Small	intestine
19	chr5:40686400-40690600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:40686800-40690800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:40686800-40692000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr5:40687000-40690000	Enhancers	Colon Smooth Muscle	Colon
23	chr5:40687400-40690400	Genic enhancers	HSMM	muscle
24	chr5:40687600-40690600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:40687600-40690600	Enhancers	HMEC	breast
26	chr5:40687800-40690200	Enhancers	Osteobl	bone
27	chr5:40687800-40690600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:40687800-40691800	Weak transcription	Small Intestine	intestine
29	chr5:40688000-40690000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:40688000-40690400	Enhancers	NH-A	brain
31	chr5:40688000-40691600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr5:40688200-40690600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:40688200-40691000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr5:40688200-40693800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
35	chr5:40688400-40690200	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr5:40688400-40696400	Weak transcription	Liver	Liver
37	chr5:40688400-40700400	Weak transcription	Stomach Mucosa	stomach
38	chr5:40688600-40690600	Enhancers	NHLF	lung
39	chr5:40688600-40690800	Genic enhancers	Rectal Mucosa Donor 31	rectum
40	chr5:40688600-40690800	Enhancers	NHDF-Ad	bronchial
41	chr5:40688600-40691000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr5:40688800-40690000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr5:40688800-40690000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:40688800-40690000	Weak transcription	HSMMtube	muscle
45	chr5:40688800-40690200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr5:40688800-40690800	Enhancers	A549	lung
47	chr5:40688800-40691200	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr5:40688800-40691400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr5:40688800-40691600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr5:40688800-40691800	Weak transcription	Fetal Intestine Large	intestine

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