Variant report

Variant	rs12613370
Chromosome Location	chr2:189249518-189249519
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10460383	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10931347	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10931350	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11688935	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12693496	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13014162	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34711211	1.00[ASN][1000 genomes]
rs35103373	0.81[ASN][1000 genomes]
rs35409022	0.90[ASN][1000 genomes]
rs4233800	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4278900	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4292061	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4353610	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4353611	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4446047	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4505490	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6434274	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6434275	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6434276	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6434279	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67050668	0.90[ASN][1000 genomes]
rs6711599	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723034	0.90[ASN][1000 genomes]
rs6727073	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72896867	0.81[ASN][1000 genomes]
rs72896889	0.81[ASN][1000 genomes]
rs72911485	0.81[ASN][1000 genomes]
rs72913310	0.81[ASN][1000 genomes]
rs72913317	0.81[ASN][1000 genomes]
rs72913357	0.81[ASN][1000 genomes]
rs72913372	0.81[ASN][1000 genomes]
rs7419883	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7424417	0.81[ASN][1000 genomes]
rs7559636	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7575702	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7577484	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7579249	0.81[ASN][1000 genomes]
rs7585851	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010394	chr2:188994398-189284092	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	nsv998395	chr2:189018246-189284092	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1010330	chr2:189182307-189265614	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv999135	chr2:189184937-189265614	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv534341	chr2:189200405-189368467	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv533786	chr2:189248503-189354495	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189245200-189259800	Weak transcription	Gastric	stomach
2	chr2:189246800-189250800	Weak transcription	Fetal Kidney	kidney
3	chr2:189247000-189251000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:189247200-189249600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:189247200-189250600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:189247200-189250600	Weak transcription	Psoas Muscle	Psoas
7	chr2:189247200-189252000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:189247200-189252200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:189247400-189250600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:189247600-189251000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
11	chr2:189247600-189251200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
12	chr2:189247600-189253400	Weak transcription	Left Ventricle	heart
13	chr2:189247600-189259800	Weak transcription	Pancreas	Pancrea
14	chr2:189247800-189251000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
15	chr2:189247800-189251600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:189247800-189252400	Weak transcription	Stomach Mucosa	stomach
17	chr2:189247800-189259600	Weak transcription	Fetal Heart	heart
18	chr2:189248000-189251000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
19	chr2:189248200-189251800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
20	chr2:189248200-189253800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:189248200-189254800	Weak transcription	HUVEC	blood vessel
22	chr2:189248400-189250200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:189248400-189250400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:189248400-189250400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:189248400-189250600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:189248400-189251200	Weak transcription	NHLF	lung
27	chr2:189248400-189251400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:189248400-189253200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:189248400-189255400	Weak transcription	Osteobl	bone
30	chr2:189248600-189251800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:189248800-189250000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:189248800-189251000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:189248800-189251000	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
34	chr2:189248800-189251200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
35	chr2:189248800-189251200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:189248800-189251200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
37	chr2:189248800-189251200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:189248800-189251200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:189248800-189251200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
40	chr2:189248800-189251200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:189249000-189249600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:189249000-189249600	Strong transcription	Placenta	Placenta
43	chr2:189249000-189249600	Strong transcription	Fetal Stomach	stomach
44	chr2:189249000-189250600	Strong transcription	Fetal Lung	lung
45	chr2:189249000-189251000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
46	chr2:189249000-189251000	ZNF genes & repeats	Fetal Intestine Small	intestine
47	chr2:189249000-189251200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:189249000-189251200	Strong transcription	Fetal Intestine Large	intestine
49	chr2:189249000-189251400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:189249200-189251200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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