Variant report

Variant	rs11609634
Chromosome Location	chr12:12309687-12309688
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10431302	0.81[CEU][hapmap]
rs10772536	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10772537	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10772540	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10845489	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10845491	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10845492	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10845494	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10845495	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10845501	0.80[EUR][1000 genomes]
rs11054718	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11054721	0.84[MEX][hapmap]
rs11054724	0.89[CEU][hapmap];0.84[AMR][1000 genomes]
rs11054731	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs11054754	0.80[CEU][hapmap]
rs12366664	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12823243	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17819999	1.00[LWK][hapmap];0.84[MEX][hapmap]
rs1819871	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2284396	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2302684	0.82[CEU][hapmap];0.89[CHB][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2417086	0.93[CEU][hapmap];0.84[GIH][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3782528	0.92[CEU][hapmap];0.85[AMR][1000 genomes]
rs4477532	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4763785	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4763794	0.81[CEU][hapmap]
rs4763795	0.81[CEU][hapmap]
rs6488507	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7294695	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7305037	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7956548	0.93[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7956971	0.83[EUR][1000 genomes]
rs7962366	0.81[CEU][hapmap]
rs7966410	1.00[LWK][hapmap];0.84[MEX][hapmap]
rs7979447	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9705600	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv975452	chr12:12306727-12310665	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11609634	CLEC2A	cis	parietal	SCAN
rs11609634	LRP6	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12262400-12335600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:12263800-12314600	Weak transcription	Esophagus	oesophagus
3	chr12:12264400-12311400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:12269600-12343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:12272200-12344600	Weak transcription	Primary B cells from cord blood	blood
6	chr12:12272400-12325200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr12:12274600-12313600	Weak transcription	Colonic Mucosa	Colon
8	chr12:12277600-12311600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:12278200-12310600	Weak transcription	Hela-S3	cervix
10	chr12:12279800-12311000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:12279800-12311000	Weak transcription	HMEC	breast
12	chr12:12279800-12311600	Weak transcription	Dnd41	blood
13	chr12:12279800-12313800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr12:12279800-12342800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:12281800-12335600	Weak transcription	Psoas Muscle	Psoas
16	chr12:12285000-12309800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:12285000-12311400	Weak transcription	Pancreas	Pancrea
18	chr12:12285600-12315000	Weak transcription	Fetal Heart	heart
19	chr12:12287400-12318200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:12288200-12310600	Weak transcription	Colon Smooth Muscle	Colon
21	chr12:12288200-12342800	Weak transcription	K562	blood
22	chr12:12288600-12311400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:12289400-12318200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr12:12297200-12318000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:12297600-12321400	Weak transcription	Gastric	stomach
26	chr12:12298800-12312200	Strong transcription	Fetal Intestine Large	intestine
27	chr12:12299200-12310200	Strong transcription	Fetal Muscle Leg	muscle
28	chr12:12300600-12315800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:12300800-12313200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:12302000-12310200	Weak transcription	NHDF-Ad	bronchial
31	chr12:12302000-12311400	Weak transcription	Aorta	Aorta
32	chr12:12302000-12311800	Weak transcription	Lung	lung
33	chr12:12302000-12318000	Weak transcription	Stomach Mucosa	stomach
34	chr12:12302200-12325000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr12:12302200-12338400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr12:12302400-12313000	Weak transcription	NHLF	lung
37	chr12:12302600-12311400	Weak transcription	Brain Angular Gyrus	brain
38	chr12:12302800-12311400	Weak transcription	Fetal Brain Female	brain
39	chr12:12302800-12317200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:12303600-12318200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:12303800-12311200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr12:12303800-12316200	Weak transcription	GM12878-XiMat	blood
43	chr12:12303800-12316600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr12:12303800-12335600	Weak transcription	Right Ventricle	heart
45	chr12:12304000-12310000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr12:12304000-12310200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:12304000-12310200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:12304000-12311000	Weak transcription	Adipose Nuclei	Adipose
49	chr12:12304000-12311200	Weak transcription	Osteobl	bone
50	chr12:12304000-12311600	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links