Variant report

Variant	rs10499217
Chromosome Location	chr6:140371611-140371612
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10499218	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751210	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11753982	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11754152	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11754864	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11755397	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11756192	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11758188	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11758612	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11758718	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11759030	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1324127	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1324129	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13437498	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1361247	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1408295	1.00[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs1582145	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17069446	1.00[JPT][hapmap]
rs17069692	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17214668	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17516817	1.00[JPT][hapmap]
rs17755520	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17755892	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17756503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17756562	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17756688	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17757864	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17811661	0.93[EUR][1000 genomes]
rs17811691	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17811871	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17812354	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17812384	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17812480	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17812617	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17812647	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17812736	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1890428	1.00[JPT][hapmap]
rs1933741	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs201279	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs201280	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2144168	1.00[JPT][hapmap]
rs35441484	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs477737	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4895580	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4895581	0.88[EUR][1000 genomes]
rs4896502	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs4896504	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896505	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4896506	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4896507	0.85[EUR][1000 genomes]
rs496953	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55732492	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55738757	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55834276	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55902158	0.87[EUR][1000 genomes]
rs55907136	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56022257	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56030520	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56202454	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56296431	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58650930	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs593265	0.93[EUR][1000 genomes]
rs59665575	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs597854	0.93[EUR][1000 genomes]
rs608185	0.93[EUR][1000 genomes]
rs615587	0.93[EUR][1000 genomes]
rs638899	0.93[EUR][1000 genomes]
rs645740	0.93[EUR][1000 genomes]
rs656337	0.93[EUR][1000 genomes]
rs656363	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs657276	0.93[EUR][1000 genomes]
rs659714	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs661507	0.93[EUR][1000 genomes]
rs671038	0.93[EUR][1000 genomes]
rs6913694	1.00[JPT][hapmap]
rs6925609	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72975808	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72975814	0.92[EUR][1000 genomes]
rs72988718	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72988720	0.93[EUR][1000 genomes]
rs72988721	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72988724	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72988734	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72988736	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72988741	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72988745	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72988750	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72988752	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72988753	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72988755	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72988756	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72988758	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72988759	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72988761	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72990622	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72990629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769264	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs924090	0.80[EUR][1000 genomes]
rs9484333	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9495619	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9495621	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs953112	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1019508	chr6:140317472-140434466	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1022987	chr6:140344229-140463916	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10499217	PBOV1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140365600-140373000	Weak transcription	Fetal Intestine Small	intestine
2	chr6:140365600-140374200	Weak transcription	A549	lung
3	chr6:140366600-140372000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:140366800-140372200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:140369400-140374600	Enhancers	Hela-S3	cervix
6	chr6:140369800-140372200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:140370000-140373600	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr6:140370200-140373800	Enhancers	Fetal Heart	heart
9	chr6:140370400-140372400	Weak transcription	Brain Germinal Matrix	brain
10	chr6:140370600-140371800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr6:140370600-140372000	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr6:140370600-140372400	Enhancers	H1 Cell Line	embryonic stem cell
13	chr6:140370600-140372600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:140370600-140373000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:140370600-140374800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:140370600-140375400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr6:140370800-140371800	Enhancers	H9 Cell Line	embryonic stem cell
18	chr6:140370800-140371800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr6:140370800-140372000	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr6:140370800-140372200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:140370800-140372400	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr6:140370800-140373000	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr6:140370800-140373400	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr6:140370800-140373800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:140370800-140374800	Enhancers	Placenta Amnion	Placenta Amnion
26	chr6:140370800-140375000	Enhancers	NH-A	brain
27	chr6:140371000-140371800	Enhancers	Fetal Thymus	thymus
28	chr6:140371000-140372000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:140371200-140371800	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr6:140371200-140371800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:140371200-140372200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:140371200-140374000	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr6:140371200-140374600	Enhancers	Fetal Brain Male	brain
34	chr6:140371200-140374600	Enhancers	Osteobl	bone
35	chr6:140371400-140371800	Active TSS	Brain Anterior Caudate	brain
36	chr6:140371400-140371800	Active TSS	Fetal Brain Female	brain
37	chr6:140371400-140373400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:140371400-140373600	Enhancers	HSMM	muscle
39	chr6:140371400-140374800	Enhancers	HMEC	breast
40	chr6:140371400-140374800	Enhancers	NHEK	skin
41	chr6:140371400-140374800	Enhancers	NHLF	lung
42	chr6:140371400-140375000	Enhancers	NHDF-Ad	bronchial
43	chr6:140371600-140371800	Bivalent Enhancer	K562	blood
44	chr6:140371600-140372000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr6:140371600-140372200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr6:140371600-140372600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:140371600-140372800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:140371600-140374600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:140371600-140375400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:140371600-140379400	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links