Variant report

Variant	rs12999503
Chromosome Location	chr2:153283775-153283776
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11694392	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11696004	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12693362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13388095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16831065	1.00[JPT][hapmap]
rs16831093	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16831100	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16831118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34006820	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35662043	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3811576	0.81[CEU][hapmap];0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6757782	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7587450	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7601047	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv875291	chr2:153251742-153339823	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	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

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153264200-153288200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:153272600-153284800	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:153272600-153285400	Weak transcription	Gastric	stomach
4	chr2:153272800-153288200	Weak transcription	Right Atrium	heart
5	chr2:153278200-153287400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:153278400-153286000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:153278400-153289800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:153278600-153284200	Weak transcription	Fetal Lung	lung
9	chr2:153278600-153288000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:153278800-153288200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:153278800-153290600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:153278800-153291200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:153279000-153284600	Weak transcription	Stomach Mucosa	stomach
14	chr2:153279000-153287400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:153279000-153287600	Weak transcription	Adipose Nuclei	Adipose
16	chr2:153279200-153288200	Weak transcription	Left Ventricle	heart
17	chr2:153279400-153285400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:153279400-153288200	Weak transcription	Placenta	Placenta
19	chr2:153279400-153288200	Weak transcription	Lung	lung
20	chr2:153280000-153305200	Enhancers	Brain Cingulate Gyrus	brain
21	chr2:153280200-153284400	Weak transcription	Hela-S3	cervix
22	chr2:153280400-153287600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:153280600-153284400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:153280600-153286400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:153280600-153287400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:153280800-153286400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr2:153280800-153288400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:153281200-153285400	Weak transcription	Psoas Muscle	Psoas
29	chr2:153281400-153283800	Enhancers	Brain Angular Gyrus	brain
30	chr2:153281400-153285800	Enhancers	Brain Hippocampus Middle	brain
31	chr2:153281400-153285800	Enhancers	Brain Substantia Nigra	brain
32	chr2:153281600-153285400	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr2:153281600-153291600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:153282200-153283800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr2:153282200-153285000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:153282400-153285000	Enhancers	NHEK	skin
37	chr2:153282400-153286200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:153282600-153283800	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr2:153282600-153285400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:153282600-153304400	Enhancers	Brain Anterior Caudate	brain
41	chr2:153282800-153283800	Enhancers	Osteobl	bone
42	chr2:153282800-153285600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:153283000-153283800	Enhancers	Muscle Satellite Cultured Cells	--
44	chr2:153283000-153284200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:153283000-153284800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:153283000-153284800	Weak transcription	Fetal Brain Male	brain
47	chr2:153283000-153285400	Weak transcription	NHDF-Ad	bronchial
48	chr2:153283000-153285800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:153283000-153288200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:153283200-153284200	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links