Variant report

Variant	rs12260189
Chromosome Location	chr10:38301043-38301044
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:38301032-38301271	HepG2	liver:	n/a	n/a
2	POLR2A	chr10:38301037-38301063	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr10:38300887-38301227	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:38298494..38301362-chr10:38382665..38385531,3	K562	blood:
2	chr10:38299411..38301761-chr10:38382405..38384673,2	MCF-7	breast:
3	chr10:38299349..38301423-chr10:38382665..38385531,5	K562	blood:
4	chr10:38298279..38301657-chr10:38381478..38384966,6	MCF-7	breast:
5	chr10:38264914..38266697-chr10:38299677..38301313,2	K562	blood:

Variant related genes	Relation type
ZNF33A	TF binding region
ENSG00000075407	Chromatin interaction
ENSG00000175395	Chromatin interaction
ENSG00000226447	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10827830	1.00[EUR][1000 genomes]
rs10827834	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10827837	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10827838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011375	1.00[EUR][1000 genomes]
rs11011376	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11011385	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011391	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11011393	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011403	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011412	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011415	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011417	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11011428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011429	1.00[EUR][1000 genomes]
rs11011430	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011437	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011438	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11812927	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11813723	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11813932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11814622	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11816307	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11816860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11817782	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11818933	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12240311	1.00[EUR][1000 genomes]
rs12241614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12242343	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12245586	1.00[EUR][1000 genomes]
rs12248857	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12250395	1.00[EUR][1000 genomes]
rs12252754	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12256181	1.00[EUR][1000 genomes]
rs12256794	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12256916	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12257902	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12258024	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs12258128	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12260310	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12262814	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12262927	1.00[EUR][1000 genomes]
rs12266728	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12267847	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12269398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12770231	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12773340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12777107	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12779056	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2023432	1.00[EUR][1000 genomes]
rs34222428	1.00[EUR][1000 genomes]
rs34445730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34591573	1.00[EUR][1000 genomes]
rs34918037	1.00[EUR][1000 genomes]
rs34964888	1.00[EUR][1000 genomes]
rs35006520	1.00[EUR][1000 genomes]
rs35246660	1.00[EUR][1000 genomes]
rs35404142	1.00[EUR][1000 genomes]
rs57753536	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60538050	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71491210	1.00[EUR][1000 genomes]
rs71491212	1.00[EUR][1000 genomes]
rs71491214	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71491223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71491227	1.00[EUR][1000 genomes]
rs71491228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71491229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9651365	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045684	chr10:37765361-38426204	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv540564	chr10:37765361-38426204	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1040704	chr10:37940024-38451917	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1051121	chr10:38155991-38426204	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv540565	chr10:38155991-38426204	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv534122	chr10:38240258-38356008	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv540566	chr10:38301001-38680127	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38298800-38301400	Active TSS	K562	blood
2	chr10:38299000-38301200	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr10:38299000-38301200	Active TSS	Brain Germinal Matrix	brain
4	chr10:38299000-38301200	Active TSS	Fetal Intestine Large	intestine
5	chr10:38299000-38301200	Active TSS	Fetal Kidney	kidney
6	chr10:38299000-38301200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr10:38299000-38301600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr10:38300000-38301200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr10:38300400-38301200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr10:38300400-38301200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr10:38300400-38301200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr10:38300400-38301200	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr10:38300400-38301600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr10:38300400-38304200	Weak transcription	Esophagus	oesophagus
15	chr10:38300400-38305200	Weak transcription	Lung	lung
16	chr10:38300400-38305800	Weak transcription	Ovary	ovary
17	chr10:38300400-38305800	Weak transcription	Spleen	Spleen
18	chr10:38300400-38306000	Weak transcription	Small Intestine	intestine
19	chr10:38300400-38319600	Weak transcription	Gastric	stomach
20	chr10:38300600-38301200	Enhancers	Brain Substantia Nigra	brain
21	chr10:38300600-38301400	Enhancers	Primary B cells from peripheral blood	blood
22	chr10:38300600-38301600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr10:38300600-38301600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr10:38300600-38301600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr10:38300600-38302000	Flanking Active TSS	Dnd41	blood
26	chr10:38300600-38303600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr10:38300600-38304000	Weak transcription	Aorta	Aorta
28	chr10:38300600-38305200	Weak transcription	Left Ventricle	heart
29	chr10:38300600-38306000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr10:38300600-38306000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr10:38300600-38318000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr10:38300600-38331600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr10:38300600-38336000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr10:38300600-38339400	Weak transcription	Psoas Muscle	Psoas
35	chr10:38300800-38301200	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr10:38300800-38301200	Enhancers	Brain Anterior Caudate	brain
37	chr10:38300800-38301200	Enhancers	Brain Cingulate Gyrus	brain
38	chr10:38300800-38301200	Enhancers	Colon Smooth Muscle	Colon
39	chr10:38300800-38301200	Enhancers	Fetal Heart	heart
40	chr10:38300800-38301200	Enhancers	Fetal Lung	lung
41	chr10:38300800-38301200	Enhancers	Placenta	Placenta
42	chr10:38300800-38301200	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr10:38300800-38301200	Flanking Active TSS	A549	lung
44	chr10:38300800-38301200	Flanking Active TSS	GM12878-XiMat	blood
45	chr10:38300800-38301200	Flanking Active TSS	HepG2	liver
46	chr10:38300800-38301200	Enhancers	HUVEC	blood vessel
47	chr10:38300800-38301200	Flanking Active TSS	NHEK	skin
48	chr10:38300800-38301200	Enhancers	NHLF	lung
49	chr10:38300800-38301400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr10:38300800-38301400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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