Variant report

Variant	rs12296239
Chromosome Location	chr12:12273437-12273438
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10082834	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466847	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466848	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772531	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10845497	1.00[ASN][1000 genomes]
rs10845499	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10845500	1.00[ASN][1000 genomes]
rs11054695	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054696	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054702	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054705	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054706	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054707	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054709	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054710	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054713	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054720	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11054729	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11054732	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs11054746	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[ASN][1000 genomes]
rs11054767	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1123213	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11829211	1.00[ASN][1000 genomes]
rs11831610	1.00[ASN][1000 genomes]
rs12305378	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306293	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306537	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307111	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[ASN][1000 genomes]
rs12309246	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309338	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12309495	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12310020	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311202	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311922	1.00[ASN][1000 genomes]
rs12316043	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422890	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424332	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424361	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425185	1.00[ASN][1000 genomes]
rs12425699	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13377971	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16907789	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757828	1.00[CHD][hapmap]
rs2448053	1.00[CHD][hapmap]
rs28448423	1.00[ASN][1000 genomes]
rs56259928	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58682800	1.00[ASN][1000 genomes]
rs59386755	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308022	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs7311064	1.00[ASN][1000 genomes]
rs7957531	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7973718	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs7978064	0.82[CEU][hapmap];0.87[MEX][hapmap]
rs7979919	1.00[ASN][1000 genomes]
rs9630249	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630250	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630266	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12235400-12278800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr12:12252800-12276200	Weak transcription	Fetal Heart	heart
3	chr12:12258200-12274000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:12260800-12276000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:12260800-12277000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:12261000-12276800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:12261200-12274000	Weak transcription	Ovary	ovary
8	chr12:12261200-12277000	Weak transcription	Hela-S3	cervix
9	chr12:12261400-12275800	Weak transcription	NH-A	brain
10	chr12:12261600-12301400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:12261800-12288000	Weak transcription	Gastric	stomach
12	chr12:12262200-12277200	Weak transcription	Brain Germinal Matrix	brain
13	chr12:12262400-12277200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:12262400-12335600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:12262800-12284800	Weak transcription	Aorta	Aorta
16	chr12:12263800-12314600	Weak transcription	Esophagus	oesophagus
17	chr12:12264000-12301400	Weak transcription	Right Ventricle	heart
18	chr12:12264200-12284600	Weak transcription	Pancreas	Pancrea
19	chr12:12264400-12284800	Weak transcription	Lung	lung
20	chr12:12264400-12311400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:12264600-12276400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:12265400-12279000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:12265600-12303400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:12266000-12274000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:12266800-12276000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:12266800-12276400	Weak transcription	HMEC	breast
27	chr12:12267200-12276200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr12:12267800-12273800	Weak transcription	Fetal Stomach	stomach
29	chr12:12267800-12282400	Weak transcription	Fetal Intestine Small	intestine
30	chr12:12267800-12301600	Weak transcription	NHLF	lung
31	chr12:12268200-12277400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:12268400-12279000	Weak transcription	Colon Smooth Muscle	Colon
33	chr12:12268600-12273600	Weak transcription	Brain Angular Gyrus	brain
34	chr12:12268800-12276400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr12:12268800-12301600	Weak transcription	Brain Substantia Nigra	brain
36	chr12:12269000-12276400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:12269200-12276400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr12:12269200-12279600	Weak transcription	Fetal Brain Male	brain
39	chr12:12269600-12343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr12:12270200-12277400	Weak transcription	HUVEC	blood vessel
41	chr12:12270400-12274000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:12270400-12277600	Weak transcription	NHDF-Ad	bronchial
43	chr12:12270600-12274000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:12270600-12284800	Weak transcription	Spleen	Spleen
45	chr12:12271000-12284400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:12271000-12301600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr12:12271200-12274800	Weak transcription	Dnd41	blood
48	chr12:12271200-12280600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr12:12271400-12281200	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:12271400-12286600	Strong transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links