Variant report

Variant	rs2388060
Chromosome Location	chr12:39279480-39279481
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10506129	0.87[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10876149	0.84[ASW][hapmap];0.87[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876163	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169387	0.84[ASW][hapmap]
rs11169508	0.84[ASW][hapmap]
rs11169769	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169801	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169838	1.00[LWK][hapmap]
rs11169879	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169908	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11609849	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11612004	0.84[ASW][hapmap]
rs11613205	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11615668	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12812262	0.87[CEU][hapmap]
rs12827647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554550	0.84[ASW][hapmap]
rs17464772	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17465893	0.95[CEU][hapmap]
rs17523988	0.84[ASW][hapmap];0.87[CEU][hapmap];0.86[GIH][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2056159	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2388061	1.00[LWK][hapmap]
rs34204495	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36035670	0.85[EUR][1000 genomes]
rs4332556	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768548	0.82[CEU][hapmap]
rs6580755	0.84[ASW][hapmap]
rs7960621	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7967776	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047623	chr12:39187817-39539939	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3389115	chr12:39221256-39448458	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39204000-39284800	Weak transcription	Lung	lung
2	chr12:39239200-39284000	Weak transcription	Hela-S3	cervix
3	chr12:39253000-39279600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:39261800-39279600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:39266400-39283200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:39269800-39285800	Weak transcription	Osteobl	bone
7	chr12:39271800-39297200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:39272600-39284000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:39274400-39279800	Weak transcription	A549	lung
10	chr12:39276400-39283400	Weak transcription	Left Ventricle	heart
11	chr12:39276600-39282800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:39276800-39281800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr12:39276800-39283800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr12:39277200-39279600	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr12:39277600-39282000	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr12:39277800-39287200	Weak transcription	Aorta	Aorta
17	chr12:39278200-39279600	Weak transcription	Colonic Mucosa	Colon
18	chr12:39278200-39284400	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr12:39278400-39279800	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:39278400-39279800	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr12:39278800-39279600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:39278800-39281400	Enhancers	Liver	Liver
23	chr12:39279400-39279800	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr12:39279400-39280000	Enhancers	Stomach Mucosa	stomach
25	chr12:39279400-39280200	Enhancers	Right Atrium	heart

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