Variant report

Variant	rs10774035
Chromosome Location	chr12:2368674-2368675
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1006737	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1024582	0.92[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10744560	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10774034	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs10774036	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10774037	0.81[MEX][hapmap]
rs10848642	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs11062159	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs11062161	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs11062162	0.81[ASN][1000 genomes]
rs11062166	0.81[ASN][1000 genomes]
rs11062170	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1108073	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs1108074	0.82[CHB][hapmap]
rs1108075	0.81[ASN][1000 genomes]
rs1108221	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs1108222	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs12311439	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12315711	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12424245	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2007044	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs2159100	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2190771	0.81[ASN][1000 genomes]
rs3922316	0.81[ASN][1000 genomes]
rs4298967	0.92[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4765904	0.83[CEU][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4765905	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4765914	0.81[MEX][hapmap]
rs7297582	0.88[CHD][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap]
rs758170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs769087	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7965923	0.90[EUR][1000 genomes];0.91[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	nsv1040370	chr12:2021395-2671017	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv948400	chr12:2022411-2601363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10774035	SLC6A12	cis	parietal	SCAN
rs10774035	CACNA1C	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2361400-2370600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:2365000-2369200	Enhancers	Osteobl	bone
3	chr12:2365200-2369000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:2365200-2369000	Weak transcription	Aorta	Aorta
5	chr12:2365200-2369000	Weak transcription	Lung	lung
6	chr12:2365200-2369000	Weak transcription	Right Atrium	heart
7	chr12:2365200-2369200	Weak transcription	Fetal Intestine Large	intestine
8	chr12:2365200-2371400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:2365200-2372800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:2365200-2373000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:2365200-2373400	Weak transcription	Adipose Nuclei	Adipose
12	chr12:2365200-2373600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr12:2365200-2374200	Weak transcription	Brain Anterior Caudate	brain
14	chr12:2365400-2369000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:2365400-2369000	Weak transcription	Spleen	Spleen
16	chr12:2365400-2369200	Weak transcription	Fetal Intestine Small	intestine
17	chr12:2365400-2373200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr12:2365400-2374200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:2365400-2374400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:2365400-2374800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:2365400-2376000	Weak transcription	Brain Angular Gyrus	brain
22	chr12:2366000-2373200	Weak transcription	HSMMtube	muscle
23	chr12:2366200-2369400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr12:2366400-2371000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:2366400-2373200	Weak transcription	NH-A	brain
26	chr12:2366800-2368800	Enhancers	Fetal Heart	heart
27	chr12:2366800-2370000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:2367000-2370000	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr12:2367200-2369200	Enhancers	NHDF-Ad	bronchial
30	chr12:2367200-2369600	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr12:2367200-2370000	Enhancers	Primary hematopoietic stem cells	blood
32	chr12:2367400-2370800	Weak transcription	NHLF	lung
33	chr12:2367600-2369400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:2367600-2369400	Enhancers	Primary T cells from cord blood	blood
35	chr12:2367800-2369600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:2368000-2368800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:2368000-2369200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:2368000-2369400	Enhancers	Fetal Thymus	thymus
39	chr12:2368000-2373000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr12:2368200-2368800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:2368200-2368800	Enhancers	Fetal Muscle Leg	muscle
42	chr12:2368200-2369400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:2368200-2369400	Enhancers	Fetal Lung	lung
44	chr12:2368200-2369400	Enhancers	Thymus	Thymus
45	chr12:2368200-2369800	Enhancers	Left Ventricle	heart
46	chr12:2368200-2370000	Enhancers	Right Ventricle	heart
47	chr12:2368400-2368800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr12:2368400-2369000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr12:2368400-2369000	Enhancers	Colon Smooth Muscle	Colon
50	chr12:2368400-2369200	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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