Variant report

Variant	rs2408185
Chromosome Location	chr12:45613828-45613829
allele	C/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	RUNX3	chr12:45613477-45614117	GM12878	blood:	n/a	chr12:45613637-45613654
2	GTF2F1	chr12:45613727-45614171	Hela-S3	cervix:	n/a	n/a
3	EBF1	chr12:45613589-45614104	GM12878	blood:	n/a	chr12:45613725-45613736
4	WRNIP1	chr12:45613389-45614010	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:45609724..45611735-chr12:45612584..45615895,4	MCF-7	breast:
2	chr12:45613308..45615413-chr12:45619971..45621498,2	K562	blood:
3	chr12:45612938..45614519-chr12:45750771..45753564,2	MCF-7	breast:

Variant related genes	Relation type
PLEKHA8P1	TF binding region
ENSG00000134297	Chromatin interaction
ENSG00000177119	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1025090	0.82[JPT][hapmap]
rs10437984	0.91[EUR][1000 genomes]
rs10459293	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10459294	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10459295	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10492284	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10785556	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10785557	0.91[EUR][1000 genomes]
rs10785569	0.80[JPT][hapmap]
rs10880757	0.90[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10880758	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10880760	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10880761	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10880762	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs10880763	0.91[EUR][1000 genomes]
rs10880764	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs10880765	0.88[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs10880766	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10880768	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs10880775	0.81[JPT][hapmap]
rs11182898	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11182899	0.93[ASN][1000 genomes]
rs11182903	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11182904	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11182905	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs11182908	0.81[EUR][1000 genomes]
rs11182912	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11182913	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11182915	0.81[AFR][1000 genomes]
rs11182916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182917	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182918	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs11182919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11182921	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182922	0.91[EUR][1000 genomes]
rs11182923	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11182927	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182931	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182935	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11182936	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11182938	0.91[EUR][1000 genomes]
rs11182939	0.91[EUR][1000 genomes]
rs11182940	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11182941	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11182942	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11182943	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11182944	0.91[EUR][1000 genomes]
rs11182946	0.91[EUR][1000 genomes]
rs11182947	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11182949	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs11182951	0.84[CHB][hapmap]
rs11182953	0.89[ASN][1000 genomes]
rs11182954	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11182955	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11182957	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11182961	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11182965	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11182981	1.00[JPT][hapmap]
rs11182983	0.81[JPT][hapmap]
rs11182986	0.80[JPT][hapmap]
rs11182988	0.80[JPT][hapmap]
rs11182989	0.81[JPT][hapmap]
rs11182990	0.81[JPT][hapmap]
rs11561532	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11610233	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11611509	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11612203	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11614082	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11614089	0.84[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs11615850	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12226944	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12227678	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12228399	0.82[ASN][1000 genomes]
rs12228733	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12230322	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs12231753	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs12299174	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12320168	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs12320437	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12322087	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12814332	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12815115	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12815334	0.89[ASN][1000 genomes]
rs12815723	0.89[ASN][1000 genomes]
rs12818421	0.86[ASN][1000 genomes]
rs12822746	0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12828052	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13378014	0.80[JPT][hapmap]
rs17095551	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17095557	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052602	0.91[EUR][1000 genomes]
rs2052603	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs2408184	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34024171	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35032811	0.82[ASN][1000 genomes]
rs35054776	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35588430	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35660715	0.91[EUR][1000 genomes]
rs3759077	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759080	0.91[EUR][1000 genomes]
rs3759081	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57560057	0.89[ASN][1000 genomes]
rs57797434	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61923810	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61923825	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61923830	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138983	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7954282	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7963038	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs7963057	0.91[EUR][1000 genomes]
rs9739519	0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050923	chr12:45581310-45808289	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2408185	TMEM16F	cis	multi-tissue	Pritchard

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45611000-45614400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr12:45611000-45617600	Weak transcription	Gastric	stomach
3	chr12:45611000-45624800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:45611200-45614600	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr12:45611200-45614800	Weak transcription	Pancreas	Pancrea
6	chr12:45611200-45628000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:45611400-45614000	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr12:45611400-45614000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr12:45611400-45614800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:45611400-45615800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:45611600-45614200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:45611600-45629400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr12:45611800-45614400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr12:45611800-45615200	Enhancers	Fetal Lung	lung
15	chr12:45611800-45615600	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr12:45611800-45615600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:45611800-45624800	Weak transcription	HSMM	muscle
18	chr12:45612000-45614000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:45612000-45614000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr12:45612000-45614000	Enhancers	Left Ventricle	heart
21	chr12:45612000-45614400	Enhancers	Fetal Heart	heart
22	chr12:45612000-45614600	Enhancers	Hela-S3	cervix
23	chr12:45612000-45614800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:45612000-45615600	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr12:45612000-45617600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:45612200-45614000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:45612200-45614000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:45612200-45614200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:45612200-45614200	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr12:45612200-45614400	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr12:45612200-45614800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:45612200-45614800	Enhancers	Fetal Stomach	stomach
33	chr12:45612200-45615000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:45612200-45615000	Enhancers	Placenta	Placenta
35	chr12:45612200-45615400	Enhancers	Colon Smooth Muscle	Colon
36	chr12:45612200-45615400	Enhancers	Placenta Amnion	Placenta Amnion
37	chr12:45612200-45617800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:45612200-45621200	Weak transcription	Fetal Brain Female	brain
39	chr12:45612400-45614000	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr12:45612400-45614000	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr12:45612400-45614000	Weak transcription	Brain Hippocampus Middle	brain
42	chr12:45612400-45614200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:45612400-45614200	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr12:45612400-45614200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:45612400-45614200	Enhancers	Liver	Liver
46	chr12:45612400-45614400	Enhancers	Fetal Intestine Small	intestine
47	chr12:45612400-45614800	Enhancers	Duodenum Mucosa	Duodenum
48	chr12:45612400-45615400	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr12:45612400-45617800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr12:45612400-45624800	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links