Variant report

Variant	rs2209661
Chromosome Location	chr12:29762976-29762977
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10400534	0.82[JPT][hapmap]
rs10400541	0.80[JPT][hapmap]
rs10492312	0.95[JPT][hapmap]
rs10771550	0.93[JPT][hapmap]
rs10771553	0.92[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11050285	0.95[JPT][hapmap]
rs11050308	0.95[JPT][hapmap]
rs12372765	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1326758	0.81[JPT][hapmap]
rs1409615	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs148898	0.91[JPT][hapmap]
rs1529908	0.94[JPT][hapmap]
rs159685	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs159689	0.95[JPT][hapmap]
rs159695	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs159696	0.81[JPT][hapmap]
rs159698	0.95[JPT][hapmap]
rs159699	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs159700	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs159712	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs159713	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs159716	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs167253	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs177254	0.95[JPT][hapmap]
rs1863224	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2081429	0.95[JPT][hapmap]
rs213539	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2148534	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2194819	0.81[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap]
rs2209660	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209662	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2225065	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2243623	0.95[JPT][hapmap]
rs2254945	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2432958	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2766599	0.95[JPT][hapmap]
rs2766601	0.95[JPT][hapmap]
rs2766602	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2766604	0.95[JPT][hapmap]
rs299454	0.91[JPT][hapmap]
rs299467	0.91[JPT][hapmap]
rs299470	0.91[JPT][hapmap]
rs299471	0.86[JPT][hapmap]
rs299479	0.91[JPT][hapmap]
rs299487	0.91[JPT][hapmap]
rs3910440	0.91[JPT][hapmap]
rs3910441	0.91[JPT][hapmap]
rs4931205	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7311193	0.95[JPT][hapmap]
rs7959535	0.96[CEU][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7960236	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7960782	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7965227	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7976832	0.84[CEU][hapmap]
rs994171	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv469190	chr12:29612425-29811471	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv557917	chr12:29612425-29811471	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1053629	chr12:29680163-29826626	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1051913	chr12:29741676-29770807	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv870004	chr12:29762415-29825798	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2209661	FGD4	cis	cerebellum	SCAN
rs2209661	FGFR1OP2	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29716200-29764800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:29731800-29769600	Weak transcription	Hela-S3	cervix
3	chr12:29743200-29769800	Weak transcription	NHLF	lung
4	chr12:29744400-29790800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:29744600-29765400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:29744600-29791000	Weak transcription	Fetal Muscle Leg	muscle
7	chr12:29744800-29764600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr12:29744800-29778200	Weak transcription	Ovary	ovary
9	chr12:29752600-29763000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:29752600-29763600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:29752600-29764600	Weak transcription	HSMMtube	muscle
12	chr12:29752600-29765600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:29752600-29768400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:29752600-29778200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:29753600-29764800	Weak transcription	NHDF-Ad	bronchial
16	chr12:29755800-29763400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:29756200-29766000	Weak transcription	HSMM	muscle
18	chr12:29757200-29763400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:29757200-29766200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:29757600-29765800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:29759000-29763600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:29760400-29763400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:29760400-29787400	Weak transcription	Adipose Nuclei	Adipose
24	chr12:29760800-29765400	Enhancers	Fetal Heart	heart
25	chr12:29760800-29767000	Weak transcription	Pancreas	Pancrea
26	chr12:29761600-29763200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr12:29761600-29763800	Enhancers	Aorta	Aorta
28	chr12:29761600-29763800	Enhancers	Left Ventricle	heart
29	chr12:29761800-29763800	Enhancers	Right Ventricle	heart
30	chr12:29761800-29764000	Enhancers	Right Atrium	heart
31	chr12:29761800-29778000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr12:29762000-29763200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:29762200-29763000	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr12:29762200-29763200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr12:29762200-29763200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr12:29762400-29763000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:29762400-29763600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:29762400-29764000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:29762400-29765200	Enhancers	Liver	Liver
40	chr12:29762400-29765200	Enhancers	Colon Smooth Muscle	Colon
41	chr12:29762400-29769600	Weak transcription	HMEC	breast
42	chr12:29762600-29763000	Genic enhancers	Spleen	Spleen
43	chr12:29762600-29763200	ZNF genes & repeats	Lung	lung
44	chr12:29762600-29763800	Enhancers	Gastric	stomach
45	chr12:29762600-29763800	Enhancers	Stomach Smooth Muscle	stomach
46	chr12:29762600-29770400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:29762800-29763000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr12:29762800-29763000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:29762800-29763200	Enhancers	Psoas Muscle	Psoas
50	chr12:29762800-29763200	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links