Variant report

Variant	rs4315964
Chromosome Location	chr5:40702396-40702397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10056345	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10060234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10064175	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1057631	0.81[CEU][hapmap]
rs1070446	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs10737963	0.83[CEU][hapmap]
rs1097546	0.85[ASN][1000 genomes]
rs13354346	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13355305	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs154280	0.85[ASN][1000 genomes]
rs154284	0.85[ASN][1000 genomes]
rs1644962	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs171605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs192219	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs193864	0.83[ASN][1000 genomes]
rs193866	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2161521	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249413	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs249416	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs249420	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs249422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249423	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];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];0.85[ASN][1000 genomes]
rs257009	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs28569300	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs29740	0.85[ASN][1000 genomes]
rs29742	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs29743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs29744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs29761	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs369940	0.85[EUR][1000 genomes]
rs4133101	0.88[CEU][hapmap]
rs4277957	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4285273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4315965	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432071	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4345353	0.84[CEU][hapmap]
rs434778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4383756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4434423	0.82[CEU][hapmap]
rs447810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs453037	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4546432	0.87[CEU][hapmap]
rs4573034	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs457776	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs4607392	0.85[CEU][hapmap]
rs461404	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59069340	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59920139	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6451535	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869461	0.80[AMR][1000 genomes]
rs6871999	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6896993	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7708680	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711806	0.85[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap]
rs7726237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7733162	0.81[AMR][1000 genomes]
rs7737044	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs837101	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv3432300	chr5:40698244-40726882	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4315964	RPL37	Cis_1M	lymphoblastoid	RTeQTL
rs4315964	TTC33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40688800-40718600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:40692400-40741200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:40692800-40702400	Weak transcription	Colonic Mucosa	Colon
4	chr5:40692800-40721000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:40692800-40733800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr5:40692800-40735000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:40693600-40727400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:40694800-40721000	Weak transcription	Thymus	Thymus
9	chr5:40695200-40715800	Weak transcription	Primary B cells from cord blood	blood
10	chr5:40695200-40727000	Weak transcription	HSMM	muscle
11	chr5:40695800-40704000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:40699000-40720800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr5:40700400-40702400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
14	chr5:40700400-40702800	ZNF genes & repeats	Primary T cells from cord blood	blood
15	chr5:40700400-40706800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:40700600-40703000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr5:40700800-40712800	Weak transcription	Gastric	stomach
18	chr5:40700800-40720600	Weak transcription	Left Ventricle	heart
19	chr5:40700800-40720800	Weak transcription	Spleen	Spleen
20	chr5:40700800-40722200	Weak transcription	Lung	lung
21	chr5:40701000-40702800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:40701000-40720800	Weak transcription	Aorta	Aorta
23	chr5:40701000-40722200	Weak transcription	Esophagus	oesophagus
24	chr5:40701400-40711400	Weak transcription	Fetal Intestine Large	intestine
25	chr5:40701600-40702400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
26	chr5:40701800-40702600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
27	chr5:40702000-40702400	ZNF genes & repeats	Rectal Smooth Muscle	rectum
28	chr5:40702000-40702400	ZNF genes & repeats	Dnd41	blood
29	chr5:40702000-40702800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr5:40702200-40702600	ZNF genes & repeats	Fetal Kidney	kidney
31	chr5:40702200-40702600	ZNF genes & repeats	Stomach Smooth Muscle	stomach

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