Variant report

Variant	rs10038669
Chromosome Location	chr5:108139943-108139944
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10044305	0.96[CHD][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes]
rs10045220	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10060694	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10062204	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs10063167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10073668	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10079165	0.90[MEX][hapmap];0.84[TSI][hapmap]
rs1022045	0.92[JPT][hapmap]
rs10477431	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1109617	0.92[JPT][hapmap]
rs11240982	0.92[JPT][hapmap]
rs11739006	0.92[JPT][hapmap]
rs12153703	0.92[JPT][hapmap]
rs13173714	0.92[JPT][hapmap]
rs13180513	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1423457	0.92[JPT][hapmap]
rs17161476	0.92[JPT][hapmap]
rs2081126	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2081129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2081130	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28637651	0.93[ASN][1000 genomes]
rs2900035	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34125469	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4604227	0.89[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4957789	0.92[JPT][hapmap]
rs6594333	0.92[JPT][hapmap]
rs6594334	0.92[JPT][hapmap]
rs6594336	0.92[JPT][hapmap]
rs6594338	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6871143	0.92[JPT][hapmap]
rs6871239	0.92[CHD][hapmap];0.92[JPT][hapmap]
rs6874229	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6875320	0.81[AMR][1000 genomes]
rs6880284	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6882107	0.96[CHD][hapmap];0.81[MEX][hapmap]
rs6889550	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6889967	0.92[JPT][hapmap]
rs6891194	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6895027	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7700630	0.82[CHD][hapmap];0.85[MEX][hapmap]
rs7709267	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7710482	0.81[AMR][1000 genomes]
rs7712834	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7712956	0.85[AMR][1000 genomes]
rs7716320	0.92[JPT][hapmap]
rs7716498	0.92[JPT][hapmap]
rs7725391	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7726708	0.85[AMR][1000 genomes]
rs7735235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9285863	0.92[JPT][hapmap]
rs9326747	0.83[AMR][1000 genomes]
rs9326748	0.89[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9885082	0.84[ASN][1000 genomes]
rs9885168	0.89[AMR][1000 genomes];0.98[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	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv471039	chr5:108133967-108245089	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108120200-108142200	Weak transcription	Aorta	Aorta
2	chr5:108120600-108146400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr5:108120800-108146400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:108124200-108141600	Weak transcription	Pancreas	Pancrea
5	chr5:108124200-108141800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:108124200-108142800	Weak transcription	Ovary	ovary
7	chr5:108124600-108146600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:108124800-108149400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr5:108133200-108146600	Weak transcription	Left Ventricle	heart
10	chr5:108133200-108146800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:108133400-108141600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:108134600-108146600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:108136400-108144600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr5:108136600-108141600	Weak transcription	Fetal Stomach	stomach
15	chr5:108137600-108141800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr5:108137600-108146000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:108137600-108153000	Weak transcription	Osteobl	bone
18	chr5:108137800-108149000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:108138000-108140000	Weak transcription	HUVEC	blood vessel
20	chr5:108138000-108153200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr5:108138600-108140400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
22	chr5:108138600-108140600	ZNF genes & repeats	Fetal Lung	lung
23	chr5:108139200-108140600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
24	chr5:108139200-108141600	ZNF genes & repeats	Primary B cells from cord blood	blood
25	chr5:108139400-108140800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:108139400-108142000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr5:108139600-108140600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:108139800-108140400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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