Variant report

Variant	rs12039337
Chromosome Location	chr1:157997084-157997085
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10430456	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12021619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12037357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12118340	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12134949	1.00[CEU][hapmap]
rs12568166	1.00[CEU][hapmap]
rs16839617	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16839627	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16839630	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16839636	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1925038	1.00[CHB][hapmap]
rs1972216	0.97[GIH][hapmap]
rs1980765	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4445460	1.00[CHB][hapmap];0.97[GIH][hapmap];0.81[TSI][hapmap]
rs4971174	1.00[CHB][hapmap]
rs4971177	0.86[GIH][hapmap]
rs4971179	0.97[GIH][hapmap];0.90[JPT][hapmap]
rs4971180	0.90[JPT][hapmap]
rs4971183	0.97[GIH][hapmap]
rs5018263	1.00[CHB][hapmap]
rs55712021	0.96[EUR][1000 genomes]
rs59269620	0.96[EUR][1000 genomes]
rs6666443	1.00[CHB][hapmap]
rs6690504	1.00[CEU][hapmap]
rs7527064	0.96[EUR][1000 genomes]
rs7530591	0.96[EUR][1000 genomes]
rs7537784	1.00[CHB][hapmap];0.93[GIH][hapmap]
rs7555783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823720	chr1:157978556-158034017	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:157985200-158006000	Weak transcription	Fetal Thymus	thymus
2	chr1:157989400-158007400	Weak transcription	Gastric	stomach
3	chr1:157991400-158000400	Weak transcription	Fetal Intestine Large	intestine
4	chr1:157991800-158002200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:157991800-158007400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:157992000-157999200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:157992800-158000600	Weak transcription	Thymus	Thymus
8	chr1:157993000-157997200	Strong transcription	NHEK	skin
9	chr1:157993000-158007400	Weak transcription	HSMMtube	muscle
10	chr1:157993000-158007600	Weak transcription	Esophagus	oesophagus
11	chr1:157993200-158007400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:157993400-157997800	Weak transcription	Hela-S3	cervix
13	chr1:157994200-157998200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr1:157994400-157997200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:157994400-157999600	Enhancers	A549	lung
16	chr1:157994600-157997600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:157995000-157997200	Genic enhancers	Stomach Smooth Muscle	stomach
18	chr1:157995000-157998000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr1:157995000-158007800	Weak transcription	Brain Germinal Matrix	brain
20	chr1:157995200-158004200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:157995400-157998000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:157995400-157999400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:157995400-158007600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:157995600-158000000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:157995600-158004400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:157995800-157997800	Weak transcription	Left Ventricle	heart
27	chr1:157995800-158000200	Weak transcription	Fetal Intestine Small	intestine
28	chr1:157995800-158000600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:157995800-158001000	Weak transcription	Fetal Brain Female	brain
30	chr1:157995800-158005600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:157995800-158007400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:157996000-157997600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:157996000-157997600	Weak transcription	Ovary	ovary
34	chr1:157996000-157998000	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr1:157996000-158000400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:157996000-158001000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:157996000-158007400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:157996000-158007400	Weak transcription	Lung	lung
39	chr1:157996200-157997200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:157996200-157997200	Enhancers	Placenta Amnion	Placenta Amnion
41	chr1:157996200-157997400	Strong transcription	Fetal Muscle Leg	muscle
42	chr1:157996200-157997600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:157996200-157998000	Weak transcription	NH-A	brain
44	chr1:157996200-158000000	Weak transcription	NHDF-Ad	bronchial
45	chr1:157996200-158000600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:157996200-158000600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:157996200-158006800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:157996200-158007600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:157996200-158007600	Weak transcription	Spleen	Spleen
50	chr1:157996400-157997400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links