Variant report

Variant	rs12992900
Chromosome Location	chr2:153361084-153361085
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10931146	0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs11897348	0.81[EUR][1000 genomes]
rs12105467	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989726	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13033468	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16831135	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16831229	1.00[CEU][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16831246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16831263	0.85[EUR][1000 genomes]
rs2881338	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34027587	0.88[EUR][1000 genomes]
rs34520795	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35455499	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4664108	0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs4664111	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4664584	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4664588	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60280470	0.85[EUR][1000 genomes]
rs67374211	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6739557	1.00[CEU][hapmap]
rs71417228	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7582905	0.81[AMR][1000 genomes];0.98[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	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2754362	chr2:153297577-153366129	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153348800-153370200	Weak transcription	Aorta	Aorta
2	chr2:153354600-153364600	Weak transcription	Left Ventricle	heart
3	chr2:153354600-153365200	Weak transcription	Pancreas	Pancrea
4	chr2:153354800-153362000	Weak transcription	Fetal Heart	heart
5	chr2:153355600-153362400	Enhancers	Fetal Brain Male	brain
6	chr2:153356000-153364600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:153356400-153361200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:153356400-153363000	Weak transcription	Small Intestine	intestine
9	chr2:153356600-153361200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:153356600-153361400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:153356600-153362000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:153356800-153364600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:153356800-153365000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:153357000-153361200	Weak transcription	NHDF-Ad	bronchial
15	chr2:153357000-153362000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:153357000-153364800	Weak transcription	Fetal Lung	lung
17	chr2:153357200-153361400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr2:153357200-153365000	Weak transcription	Fetal Stomach	stomach
19	chr2:153357400-153361400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:153357400-153364600	Weak transcription	Psoas Muscle	Psoas
21	chr2:153357400-153375200	Weak transcription	Right Atrium	heart
22	chr2:153357600-153365000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:153357600-153365200	Weak transcription	Fetal Muscle Leg	muscle
24	chr2:153357800-153362000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:153358000-153361200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:153358200-153361200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:153358200-153361200	Weak transcription	Adipose Nuclei	Adipose
28	chr2:153358200-153361200	Weak transcription	Ovary	ovary
29	chr2:153358200-153361400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr2:153358200-153364600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:153358200-153365000	Weak transcription	Fetal Brain Female	brain
32	chr2:153358600-153361200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:153358600-153361200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:153358600-153362200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:153359200-153361200	Enhancers	A549	lung
36	chr2:153359600-153362000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:153359600-153363000	Enhancers	NHEK	skin
38	chr2:153359600-153364200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:153359800-153361200	Weak transcription	Brain Angular Gyrus	brain
40	chr2:153359800-153361200	Weak transcription	Brain Substantia Nigra	brain
41	chr2:153360000-153361200	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:153360000-153361400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr2:153360000-153363200	Weak transcription	Fetal Kidney	kidney
44	chr2:153360400-153361200	Weak transcription	Hela-S3	cervix
45	chr2:153360400-153362200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr2:153360400-153362400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:153360400-153363400	Weak transcription	HepG2	liver
48	chr2:153360400-153365000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:153360600-153361200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:153360600-153364200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links