Variant report

Variant	rs888200
Chromosome Location	chr12:12555299-12555300
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12551360..12553535-chr12:12553854..12557038,3	MCF-7	breast:
2	chr12:12550258..12553161-chr12:12554299..12558157,3	MCF-7	breast:
3	chr12:12555144..12557679-chr12:12584651..12587421,2	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1019340	0.93[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1019341	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1030069	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10459098	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10743982	0.93[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10743983	0.86[ASN][1000 genomes]
rs10743985	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10772563	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10772566	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs10772567	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs10845530	0.94[CHB][hapmap]
rs10845533	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10845537	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10845539	0.87[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10845540	0.82[ASN][1000 genomes]
rs10845541	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10845542	0.82[ASN][1000 genomes]
rs10845544	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs10845545	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10845546	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10845551	0.84[CHB][hapmap]
rs11054894	0.86[ASN][1000 genomes]
rs11532310	0.86[ASN][1000 genomes]
rs11561172	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11609375	0.81[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1468876	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1544682	0.82[ASN][1000 genomes]
rs2160586	0.95[CHB][hapmap];0.94[CHD][hapmap];0.82[ASN][1000 genomes]
rs2193269	0.84[ASN][1000 genomes]
rs2193270	0.82[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2216264	0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2417187	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28853875	0.84[ASN][1000 genomes]
rs3925170	0.93[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4390432	0.89[ASN][1000 genomes]
rs4488294	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4547192	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4763825	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4763826	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4763829	0.81[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4763830	0.81[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56089442	0.83[ASN][1000 genomes]
rs56796062	0.84[ASN][1000 genomes]
rs57348917	0.83[ASN][1000 genomes]
rs6488526	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7132512	0.80[GIH][hapmap];0.81[TSI][hapmap]
rs7135655	0.84[JPT][hapmap]
rs7295080	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7300150	0.85[ASN][1000 genomes]
rs73061463	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7309503	0.87[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7309982	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7310012	0.93[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7311363	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7311364	0.81[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7313825	0.81[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7315626	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73283441	0.82[ASN][1000 genomes]
rs7953025	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7954752	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7961703	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7967038	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7967111	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[ASN][1000 genomes]
rs7967230	0.84[JPT][hapmap];0.96[MEX][hapmap];0.81[ASN][1000 genomes]
rs7967466	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7969020	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7969252	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7969270	0.89[ASN][1000 genomes]
rs7969849	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7969984	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs879445	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9645752	0.85[CHB][hapmap];0.82[CHD][hapmap];0.80[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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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 miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv1812889	chr12:12510842-12593406	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs888200	ETV6	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12521800-12556200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:12526400-12558800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr12:12532800-12556400	Weak transcription	Spleen	Spleen
4	chr12:12533400-12555800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr12:12533600-12555400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr12:12535400-12561400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr12:12537200-12576000	Weak transcription	Primary B cells from cord blood	blood
8	chr12:12538400-12555400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:12538400-12556200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:12538600-12561800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:12540200-12560600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:12540600-12556200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr12:12540800-12555400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr12:12541400-12562800	Weak transcription	Psoas Muscle	Psoas
15	chr12:12541800-12557200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr12:12543000-12558800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:12546000-12556400	Weak transcription	K562	blood
18	chr12:12547200-12556000	Weak transcription	Fetal Thymus	thymus
19	chr12:12547600-12555400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:12550000-12556000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:12550000-12556400	Weak transcription	Thymus	Thymus
22	chr12:12550400-12556200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:12551000-12555800	Weak transcription	Primary T cells from cord blood	blood
24	chr12:12551000-12559000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:12551200-12558800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:12551600-12558800	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:12551800-12555400	Weak transcription	Aorta	Aorta
28	chr12:12551800-12556200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:12552000-12555400	Weak transcription	Placenta	Placenta
30	chr12:12552000-12556000	Weak transcription	Fetal Kidney	kidney
31	chr12:12552000-12556000	Weak transcription	HUVEC	blood vessel
32	chr12:12552000-12557800	Weak transcription	Gastric	stomach
33	chr12:12552000-12558800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:12552000-12558800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:12552000-12558800	Weak transcription	Lung	lung
36	chr12:12552000-12559000	Weak transcription	HSMM	muscle
37	chr12:12552000-12559800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr12:12552000-12561400	Weak transcription	HSMMtube	muscle
39	chr12:12552000-12569000	Weak transcription	Hela-S3	cervix
40	chr12:12552200-12558600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:12552400-12556200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:12552400-12556200	Weak transcription	Pancreas	Pancrea
43	chr12:12552800-12556800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr12:12552800-12558600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr12:12552800-12558800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:12553200-12555400	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr12:12553200-12561400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr12:12553400-12555800	Weak transcription	Fetal Lung	lung
49	chr12:12553400-12556000	Weak transcription	Brain Substantia Nigra	brain
50	chr12:12553400-12556000	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links