Variant report

Variant	rs11837554
Chromosome Location	chr12:29743434-29743435
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10492311	0.85[EUR][1000 genomes]
rs11829731	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs11829994	0.82[JPT][hapmap]
rs11834102	0.87[EUR][1000 genomes]
rs11834291	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs12310251	0.82[JPT][hapmap]
rs12312423	1.00[CHB][hapmap]
rs12422557	1.00[CHB][hapmap]
rs12423770	1.00[CHB][hapmap]
rs12423941	1.00[CHB][hapmap]
rs12424239	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12424502	1.00[CHB][hapmap]
rs12425004	1.00[CHB][hapmap]
rs12810686	1.00[CHB][hapmap]
rs12811228	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12813081	1.00[CHB][hapmap]
rs12816393	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12822100	0.84[CEU][hapmap]
rs12824107	1.00[CHB][hapmap]
rs12824420	1.00[CHB][hapmap]
rs12826187	1.00[CHB][hapmap]
rs12826210	1.00[CHB][hapmap]
rs12826633	1.00[CHB][hapmap]
rs12828728	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs142565	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs159684	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159688	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs159691	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs159692	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs159693	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16934448	0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs16934474	1.00[JPT][hapmap]
rs16934556	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs16934569	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs16934597	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs16934635	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs1966531	0.84[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2288228	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs299478	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs299480	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs299484	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299485	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34318689	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3825242	1.00[CHB][hapmap]
rs55807951	0.81[EUR][1000 genomes]
rs56367916	0.82[EUR][1000 genomes]
rs57072643	0.83[EUR][1000 genomes]
rs58290227	0.83[EUR][1000 genomes]
rs59519970	0.82[EUR][1000 genomes]
rs66849216	0.81[EUR][1000 genomes]
rs67491988	0.82[EUR][1000 genomes]
rs7301943	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs73071505	0.85[EUR][1000 genomes]
rs73071510	0.85[EUR][1000 genomes]
rs73071556	0.82[EUR][1000 genomes]
rs73071582	0.83[EUR][1000 genomes]
rs7315541	0.80[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7316470	1.00[CHB][hapmap]
rs74078415	0.82[EUR][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	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

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29709800-29756200	Weak transcription	HMEC	breast
2	chr12:29716200-29764800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:29720200-29743600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:29726000-29751400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:29729400-29744000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:29731800-29769600	Weak transcription	Hela-S3	cervix
7	chr12:29735400-29745800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:29736000-29744200	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:29736000-29744200	Weak transcription	Right Atrium	heart
10	chr12:29736000-29752200	Weak transcription	HSMM	muscle
11	chr12:29736800-29762800	Weak transcription	Fetal Stomach	stomach
12	chr12:29737000-29744200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr12:29737000-29748400	Weak transcription	Spleen	Spleen
14	chr12:29737200-29744000	Weak transcription	Adipose Nuclei	Adipose
15	chr12:29737200-29744200	Weak transcription	Ovary	ovary
16	chr12:29737200-29744200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:29737200-29746800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:29737200-29748400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:29737200-29761800	Weak transcription	Right Ventricle	heart
20	chr12:29737200-29762400	Weak transcription	Colon Smooth Muscle	Colon
21	chr12:29737200-29762800	Weak transcription	Psoas Muscle	Psoas
22	chr12:29741000-29748200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:29742000-29743600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:29742200-29746000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr12:29742400-29744000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:29742400-29744200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr12:29742400-29744200	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr12:29742400-29744800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:29742600-29743600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr12:29742600-29744200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:29742600-29746200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:29742800-29744000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr12:29742800-29744000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:29742800-29744200	Weak transcription	Lung	lung
35	chr12:29742800-29744200	Weak transcription	NHDF-Ad	bronchial
36	chr12:29742800-29750200	Weak transcription	Aorta	Aorta
37	chr12:29742800-29752200	Weak transcription	HSMMtube	muscle
38	chr12:29743000-29744000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr12:29743000-29744200	Weak transcription	Fetal Muscle Leg	muscle
40	chr12:29743200-29744200	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr12:29743200-29751800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:29743200-29769800	Weak transcription	NHLF	lung
43	chr12:29743400-29743600	Enhancers	Left Ventricle	heart
44	chr12:29743400-29744000	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr12:29743400-29744200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:29743400-29744200	Weak transcription	Fetal Heart	heart
47	chr12:29743400-29744200	Weak transcription	Fetal Lung	lung
48	chr12:29743400-29744400	Enhancers	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links