Variant report

Variant	rs299483
Chromosome Location	chr12:29712087-29712088
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11050323	0.88[CHB][hapmap]
rs11829731	1.00[CHB][hapmap]
rs11834291	1.00[CHB][hapmap]
rs12822100	0.89[CHB][hapmap]
rs12826893	0.89[CHB][hapmap]
rs12826911	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12828728	0.89[CHB][hapmap]
rs142565	0.89[CHB][hapmap]
rs148897	1.00[CHB][hapmap]
rs159682	1.00[AMR][1000 genomes]
rs159683	1.00[AMR][1000 genomes]
rs159686	1.00[AMR][1000 genomes]
rs159688	0.89[CHB][hapmap]
rs159691	0.89[CHB][hapmap]
rs159692	0.89[CHB][hapmap]
rs16934418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16934523	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16934537	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16934564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs16934569	1.00[CHB][hapmap]
rs16934597	1.00[CHB][hapmap]
rs16934635	0.89[CHB][hapmap]
rs299477	0.89[CHB][hapmap]
rs299478	0.89[CHB][hapmap]
rs299482	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299485	0.89[CHB][hapmap]
rs299486	1.00[AMR][1000 genomes]
rs41322250	1.00[AMR][1000 genomes]
rs7134177	1.00[AMR][1000 genomes]
rs7301943	1.00[CHB][hapmap]
rs73263809	1.00[AMR][1000 genomes]
rs73266067	1.00[AMR][1000 genomes]
rs73266079	1.00[AMR][1000 genomes]
rs73266080	1.00[AMR][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:52 , 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	chr12:29700200-29712200	Weak transcription	Ovary	ovary
6	chr12:29700400-29719000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr12:29700400-29734000	Weak transcription	Brain Anterior Caudate	brain
8	chr12:29701000-29714200	Weak transcription	HSMMtube	muscle
9	chr12:29701200-29714400	Weak transcription	NHDF-Ad	bronchial
10	chr12:29701200-29714400	Weak transcription	NHLF	lung
11	chr12:29701200-29715200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:29701200-29715600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:29703800-29715200	Weak transcription	Fetal Muscle Leg	muscle
14	chr12:29705000-29716000	Weak transcription	Spleen	Spleen
15	chr12:29706000-29715200	Weak transcription	Colon Smooth Muscle	Colon
16	chr12:29706200-29715000	Weak transcription	Osteobl	bone
17	chr12:29706600-29716200	Weak transcription	Aorta	Aorta
18	chr12:29706800-29712200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:29706800-29712200	Weak transcription	Liver	Liver
20	chr12:29707400-29712200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:29707400-29714600	Weak transcription	Fetal Heart	heart
22	chr12:29707800-29712600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:29709800-29756200	Weak transcription	HMEC	breast
24	chr12:29710000-29712200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:29710000-29713800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:29710000-29714200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:29710000-29714200	Weak transcription	HSMM	muscle
28	chr12:29710000-29715000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:29710000-29715600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:29710200-29717800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:29711400-29713200	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr12:29711400-29716600	Enhancers	Stomach Mucosa	stomach
33	chr12:29711400-29718200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr12:29711600-29712200	Strong transcription	Hela-S3	cervix
35	chr12:29711600-29712400	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr12:29711600-29712800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:29711600-29713000	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr12:29711800-29712400	Weak transcription	Right Atrium	heart
39	chr12:29711800-29713200	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr12:29711800-29713400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:29711800-29713600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:29711800-29716600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr12:29711800-29720800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:29712000-29712200	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr12:29712000-29712400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:29712000-29712600	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr12:29712000-29712600	Active TSS	Duodenum Mucosa	Duodenum
48	chr12:29712000-29712600	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr12:29712000-29712800	Enhancers	Fetal Kidney	kidney
50	chr12:29712000-29713200	Enhancers	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links