Variant report

Variant	rs299484
Chromosome Location	chr12:29712260-29712261
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10492311	0.96[EUR][1000 genomes]
rs11829731	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs11829994	0.83[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11834102	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11834291	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs11837554	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12310251	0.83[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs12312423	1.00[CHB][hapmap]
rs12422557	1.00[CHB][hapmap]
rs12423770	1.00[CHB][hapmap]
rs12423941	1.00[CHB][hapmap]
rs12424239	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424502	1.00[CHB][hapmap]
rs12425004	1.00[CHB][hapmap]
rs12810686	1.00[CHB][hapmap]
rs12811228	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs12813081	1.00[CHB][hapmap]
rs12816393	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
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]
rs12826893	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs142565	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs148897	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs159684	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs159688	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs159691	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs159692	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs159693	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16934448	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs16934474	0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs16934556	0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs1966531	0.82[JPT][hapmap]
rs2288228	0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs299474	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs299477	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs299478	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs299480	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs299485	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34318689	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825242	1.00[CHB][hapmap]
rs56367916	0.88[EUR][1000 genomes]
rs56398900	0.91[EUR][1000 genomes]
rs57816450	0.83[EUR][1000 genomes]
rs58290227	0.87[EUR][1000 genomes]
rs59519970	0.88[EUR][1000 genomes]
rs7301943	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs73069592	0.83[EUR][1000 genomes]
rs73069593	0.83[EUR][1000 genomes]
rs73069598	0.90[EUR][1000 genomes]
rs73071505	0.96[EUR][1000 genomes]
rs73071510	0.96[EUR][1000 genomes]
rs73071517	0.91[EUR][1000 genomes]
rs73071519	0.91[EUR][1000 genomes]
rs73071533	0.91[EUR][1000 genomes]
rs73071556	0.88[EUR][1000 genomes]
rs73071582	0.87[EUR][1000 genomes]
rs7315541	0.89[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs7316470	1.00[CHB][hapmap]
rs74078415	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29665400-29725400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:29668800-29716600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:29698200-29712600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:29699400-29715800	Weak transcription	Right Ventricle	heart
5	chr12:29700400-29719000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr12:29700400-29734000	Weak transcription	Brain Anterior Caudate	brain
7	chr12:29701000-29714200	Weak transcription	HSMMtube	muscle
8	chr12:29701200-29714400	Weak transcription	NHDF-Ad	bronchial
9	chr12:29701200-29714400	Weak transcription	NHLF	lung
10	chr12:29701200-29715200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:29701200-29715600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:29703800-29715200	Weak transcription	Fetal Muscle Leg	muscle
13	chr12:29705000-29716000	Weak transcription	Spleen	Spleen
14	chr12:29706000-29715200	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:29706200-29715000	Weak transcription	Osteobl	bone
16	chr12:29706600-29716200	Weak transcription	Aorta	Aorta
17	chr12:29707400-29714600	Weak transcription	Fetal Heart	heart
18	chr12:29707800-29712600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:29709800-29756200	Weak transcription	HMEC	breast
20	chr12:29710000-29713800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr12:29710000-29714200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:29710000-29714200	Weak transcription	HSMM	muscle
23	chr12:29710000-29715000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:29710000-29715600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:29710200-29717800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:29711400-29713200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr12:29711400-29716600	Enhancers	Stomach Mucosa	stomach
28	chr12:29711400-29718200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr12:29711600-29712400	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr12:29711600-29712800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:29711600-29713000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr12:29711800-29712400	Weak transcription	Right Atrium	heart
33	chr12:29711800-29713200	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr12:29711800-29713400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:29711800-29713600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:29711800-29716600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr12:29711800-29720800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:29712000-29712400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr12:29712000-29712600	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr12:29712000-29712600	Active TSS	Duodenum Mucosa	Duodenum
41	chr12:29712000-29712600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr12:29712000-29712800	Enhancers	Fetal Kidney	kidney
43	chr12:29712000-29713200	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr12:29712000-29715200	Weak transcription	Left Ventricle	heart
45	chr12:29712000-29715600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr12:29712200-29712400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:29712200-29712400	Enhancers	Adipose Nuclei	Adipose
48	chr12:29712200-29712400	Enhancers	Small Intestine	intestine
49	chr12:29712200-29712600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:29712200-29712600	Enhancers	Liver	Liver

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