Variant report

Variant	rs12620026
Chromosome Location	chr2:148683919-148683920
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10171130	0.97[YRI][hapmap]
rs10187392	1.00[EUR][1000 genomes]
rs10497027	1.00[EUR][1000 genomes]
rs10497030	1.00[EUR][1000 genomes]
rs10928370	1.00[CEU][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13022827	1.00[CEU][hapmap];0.97[YRI][hapmap];1.00[AMR][1000 genomes]
rs13394568	1.00[EUR][1000 genomes]
rs13411618	1.00[EUR][1000 genomes]
rs1364657	0.97[YRI][hapmap]
rs1364659	1.00[EUR][1000 genomes]
rs1375858	1.00[EUR][1000 genomes]
rs1424942	0.97[YRI][hapmap]
rs1469212	1.00[CEU][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16828024	1.00[EUR][1000 genomes]
rs16828025	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16828096	1.00[EUR][1000 genomes]
rs16828177	1.00[EUR][1000 genomes]
rs16828185	1.00[EUR][1000 genomes]
rs16828243	1.00[EUR][1000 genomes]
rs16828346	1.00[EUR][1000 genomes]
rs17218917	1.00[EUR][1000 genomes]
rs2081400	1.00[MEX][hapmap]
rs2627023	1.00[EUR][1000 genomes]
rs2627027	1.00[EUR][1000 genomes]
rs2627033	1.00[MEX][hapmap]
rs2707220	1.00[EUR][1000 genomes]
rs41468049	1.00[EUR][1000 genomes]
rs4972314	1.00[CEU][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4972366	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs57204245	1.00[EUR][1000 genomes]
rs58341690	1.00[EUR][1000 genomes]
rs60605559	1.00[EUR][1000 genomes]
rs6430290	1.00[EUR][1000 genomes]
rs6731167	1.00[EUR][1000 genomes]
rs7578992	1.00[EUR][1000 genomes]
rs7581537	1.00[CEU][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7600254	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7601098	0.81[LWK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875275	chr2:148166428-148711242	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv529388	chr2:148471340-148934846	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv3392562	chr2:148476961-148843061	Strong transcription Enhancers Weak transcription Flanking Active TSS 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	15 gene(s)	inside rSNPs	diseases
5	nsv1009602	chr2:148668195-148844240	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv535967	chr2:148668195-148844240	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv1000246	chr2:148669162-148780280	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv535968	chr2:148669162-148780280	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv535969	chr2:148677122-148715921	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148637200-148752600	Weak transcription	Small Intestine	intestine
2	chr2:148646200-148684400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr2:148646600-148691000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:148647200-148719600	Weak transcription	Pancreas	Pancrea
5	chr2:148650200-148719600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:148651200-148691600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:148652800-148690000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:148652800-148693600	Weak transcription	Lung	lung
9	chr2:148653200-148692000	Weak transcription	Ovary	ovary
10	chr2:148653200-148719600	Weak transcription	Esophagus	oesophagus
11	chr2:148654000-148690000	Weak transcription	Primary T cells from cord blood	blood
12	chr2:148658800-148741600	Weak transcription	Aorta	Aorta
13	chr2:148659600-148719800	Weak transcription	Gastric	stomach
14	chr2:148661600-148718200	Weak transcription	Fetal Intestine Small	intestine
15	chr2:148663000-148692200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:148664600-148721200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:148664800-148693800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:148668600-148691800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:148670600-148690200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:148671200-148690200	Weak transcription	Placenta	Placenta
21	chr2:148671600-148690200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr2:148671800-148687400	Weak transcription	NH-A	brain
23	chr2:148671800-148690200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:148671800-148691800	Weak transcription	NHLF	lung
25	chr2:148671800-148692000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:148671800-148698800	Weak transcription	NHEK	skin
27	chr2:148671800-148719600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:148672000-148684600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr2:148672000-148691400	Weak transcription	Brain Anterior Caudate	brain
30	chr2:148672000-148692000	Weak transcription	Brain Substantia Nigra	brain
31	chr2:148672000-148692800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:148672000-148693000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:148672200-148684000	Weak transcription	Fetal Brain Female	brain
34	chr2:148672200-148688400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:148672200-148693800	Weak transcription	HUVEC	blood vessel
36	chr2:148672200-148695800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr2:148672200-148706800	Weak transcription	Brain Germinal Matrix	brain
38	chr2:148672400-148688400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:148672400-148690000	Weak transcription	A549	lung
40	chr2:148672400-148692800	Weak transcription	Stomach Mucosa	stomach
41	chr2:148672800-148688400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:148672800-148688600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:148674400-148692000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr2:148674800-148687600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:148675000-148690200	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr2:148675400-148684400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:148675400-148708800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:148676200-148722400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:148676600-148690400	Weak transcription	Primary B cells from cord blood	blood
50	chr2:148676600-148693600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links