Variant report

Variant	rs3867478
Chromosome Location	chr12:10733258-10733259
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10734838	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743910	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772315	0.83[ASN][1000 genomes]
rs10772316	0.83[ASN][1000 genomes]
rs10772317	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772318	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10772319	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772321	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772323	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772324	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772325	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10772326	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772327	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772329	0.83[ASN][1000 genomes]
rs10845153	0.88[CHB][hapmap]
rs10845161	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs10845162	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10845163	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10845164	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10845165	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10845166	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845172	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845174	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10845175	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs11053857	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs11053859	0.83[ASN][1000 genomes]
rs11053865	0.85[ASN][1000 genomes]
rs11053869	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11053870	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11053871	0.85[ASN][1000 genomes]
rs11053873	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11053874	0.85[JPT][hapmap]
rs11611202	0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs12423957	0.82[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1915322	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1915323	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2002156	0.83[ASN][1000 genomes]
rs2002157	0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2125092	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2125094	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2125095	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168750	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2417745	0.95[JPT][hapmap]
rs2417746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2417747	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2417748	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2417900	0.85[CHB][hapmap]
rs2417901	0.85[CHB][hapmap]
rs2607883	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2607888	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2607891	0.95[JPT][hapmap]
rs2607892	0.95[JPT][hapmap]
rs2607895	0.95[JPT][hapmap]
rs2607898	0.95[JPT][hapmap]
rs2682476	0.95[JPT][hapmap]
rs28701155	0.80[ASN][1000 genomes]
rs3816567	0.85[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs3983544	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3983545	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3983546	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3983547	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4237928	0.83[ASN][1000 genomes]
rs4476009	0.83[ASN][1000 genomes]
rs4536307	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4763528	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763530	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4763531	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763532	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763547	0.83[ASN][1000 genomes]
rs4763548	0.83[ASN][1000 genomes]
rs4763550	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763551	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763553	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763555	0.85[ASN][1000 genomes]
rs4763556	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4763558	0.85[ASN][1000 genomes]
rs4763559	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58917785	0.85[ASN][1000 genomes]
rs60367665	0.82[ASN][1000 genomes]
rs61913124	0.82[ASN][1000 genomes]
rs6488302	0.85[CHB][hapmap]
rs6488303	0.85[CHB][hapmap]
rs6488304	0.84[CHB][hapmap]
rs6488307	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7134658	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7134908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136310	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7136964	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7137465	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7306285	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7306724	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7311860	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7314340	0.82[AMR][1000 genomes]
rs7315514	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7955358	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7955359	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7964171	0.94[ASN][1000 genomes]
rs7964203	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7965052	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7978788	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7978850	0.81[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs7979402	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7980411	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898775	chr12:10668694-10735786	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1039120	chr12:10675930-10755446	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv832329	chr12:10677094-10845946	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10724000-10733400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:10725000-10733600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:10725600-10743600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr12:10725600-10765000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:10725800-10733800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:10725800-10743200	Weak transcription	NHDF-Ad	bronchial
7	chr12:10725800-10753400	Weak transcription	Osteobl	bone
8	chr12:10725800-10761400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:10726200-10734400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:10726400-10743200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr12:10726400-10759800	Weak transcription	NHLF	lung
12	chr12:10726800-10756600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:10729800-10733800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:10730000-10762000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:10730600-10733800	Weak transcription	Liver	Liver
16	chr12:10730600-10764800	Weak transcription	Lung	lung
17	chr12:10730800-10733800	Weak transcription	Thymus	Thymus
18	chr12:10730800-10746200	Weak transcription	Fetal Thymus	thymus
19	chr12:10730800-10758400	Weak transcription	NHEK	skin
20	chr12:10731000-10733600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:10731200-10744000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr12:10731200-10756400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr12:10731400-10733400	Weak transcription	Adipose Nuclei	Adipose
24	chr12:10731400-10753200	Weak transcription	Primary B cells from cord blood	blood
25	chr12:10731600-10733800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr12:10731600-10733800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr12:10731600-10733800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr12:10731600-10742400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr12:10731600-10760800	Weak transcription	Fetal Brain Female	brain
30	chr12:10731800-10733600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr12:10731800-10733600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr12:10731800-10733800	Weak transcription	Aorta	Aorta
33	chr12:10732000-10733400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr12:10732000-10759600	Weak transcription	Fetal Intestine Large	intestine
35	chr12:10732000-10759800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr12:10732200-10734200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:10732200-10735400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:10732200-10745800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr12:10732200-10759600	Weak transcription	Left Ventricle	heart
40	chr12:10732200-10761400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:10732200-10764800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr12:10732400-10733800	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr12:10732400-10734000	Strong transcription	Stomach Smooth Muscle	stomach
44	chr12:10732400-10734200	Strong transcription	HSMM	muscle
45	chr12:10732400-10734400	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:10732400-10743600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr12:10732400-10759600	Weak transcription	Colon Smooth Muscle	Colon
48	chr12:10732400-10764200	Weak transcription	Pancreas	Pancrea
49	chr12:10732600-10733400	Strong transcription	A549	lung
50	chr12:10732600-10734400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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