Variant report

Variant	rs7295080
Chromosome Location	chr12:12559234-12559235
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12557174..12559424-chr12:12713133..12714808,2	MCF-7	breast:
2	chr12:12550932..12553792-chr12:12558043..12559658,2	K562	blood:

Variant related genes	Relation type
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1019340	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1019341	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1030069	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10459098	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10743982	0.81[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10743983	0.84[ASN][1000 genomes]
rs10743985	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10772563	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10772566	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10772567	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10845530	0.88[CHB][hapmap]
rs10845533	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10845537	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10845539	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10845540	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10845541	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10845542	0.85[ASN][1000 genomes]
rs10845544	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10845545	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10845546	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10845551	0.89[CHB][hapmap]
rs11054894	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11054914	0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs11532310	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11561172	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11609375	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1468876	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1544682	0.85[ASN][1000 genomes]
rs2160586	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[ASN][1000 genomes]
rs2193269	0.86[ASN][1000 genomes]
rs2193270	0.81[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2216264	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2417187	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28853875	0.86[ASN][1000 genomes]
rs35908046	0.85[EUR][1000 genomes]
rs3751261	0.83[CHB][hapmap]
rs3925170	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4390432	0.91[ASN][1000 genomes]
rs4488294	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4547192	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4763825	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4763826	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4763829	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4763830	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56089442	0.85[ASN][1000 genomes]
rs56701819	0.81[ASN][1000 genomes]
rs56796062	0.86[ASN][1000 genomes]
rs56915387	0.81[ASN][1000 genomes]
rs57348917	0.86[ASN][1000 genomes]
rs6488526	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7132512	0.80[GIH][hapmap];0.89[TSI][hapmap]
rs7135655	0.84[JPT][hapmap]
rs7300150	0.87[ASN][1000 genomes]
rs73061463	0.87[ASN][1000 genomes]
rs7309503	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7309982	0.84[JPT][hapmap]
rs7310012	0.85[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7311363	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7311364	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7312010	0.81[EUR][1000 genomes]
rs7313825	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7315626	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73283441	0.81[ASN][1000 genomes]
rs7953025	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954752	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7961703	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7967038	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7967111	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs7967230	0.84[JPT][hapmap];0.96[MEX][hapmap]
rs7967466	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969020	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7969252	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7969270	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7969849	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7969984	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs879445	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs888200	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]
rs9645752	0.81[CHB][hapmap];0.81[CHD][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7295080	KLRA1	cis	cerebellum	SCAN
rs7295080	ETV6	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12535400-12561400	Weak transcription	Primary B cells from peripheral blood	blood
2	chr12:12537200-12576000	Weak transcription	Primary B cells from cord blood	blood
3	chr12:12538600-12561800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:12540200-12560600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:12541400-12562800	Weak transcription	Psoas Muscle	Psoas
6	chr12:12552000-12559800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:12552000-12561400	Weak transcription	HSMMtube	muscle
8	chr12:12552000-12569000	Weak transcription	Hela-S3	cervix
9	chr12:12553200-12561400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:12555000-12560600	Enhancers	Fetal Intestine Large	intestine
11	chr12:12555200-12560200	Enhancers	Fetal Intestine Small	intestine
12	chr12:12555200-12560800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr12:12556000-12560000	Enhancers	Liver	Liver
14	chr12:12556000-12560200	Enhancers	Stomach Mucosa	stomach
15	chr12:12556200-12560200	Enhancers	Brain Cingulate Gyrus	brain
16	chr12:12556200-12560200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr12:12556600-12559800	Weak transcription	Left Ventricle	heart
18	chr12:12556600-12561600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr12:12556800-12559800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr12:12556800-12560200	Enhancers	HepG2	liver
21	chr12:12556800-12561000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:12556800-12561800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:12557000-12559400	Weak transcription	K562	blood
24	chr12:12557000-12561000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr12:12557000-12561600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:12557200-12559800	Weak transcription	Spleen	Spleen
27	chr12:12557200-12561200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:12557200-12572400	Weak transcription	Primary T cells from cord blood	blood
29	chr12:12557400-12561000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr12:12557400-12561200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr12:12557400-12561400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr12:12557600-12560600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr12:12557600-12561000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:12557600-12561200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:12557600-12561200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:12557600-12561400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr12:12557800-12565000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:12558000-12560000	Enhancers	Brain Angular Gyrus	brain
39	chr12:12558000-12586000	Weak transcription	Pancreas	Pancrea
40	chr12:12558400-12560200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:12558600-12559400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:12558600-12559400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:12558600-12559600	Flanking Active TSS	A549	lung
44	chr12:12558800-12559400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:12558800-12559400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:12558800-12559400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:12558800-12559400	Enhancers	HMEC	breast
48	chr12:12558800-12559600	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr12:12558800-12559600	Enhancers	Fetal Lung	lung
50	chr12:12559000-12559400	Enhancers	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links