Variant report

Variant	rs11169769
Chromosome Location	chr12:39233134-39233135
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10506129	1.00[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10876086	0.84[AFR][1000 genomes]
rs10876149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169301	0.84[AFR][1000 genomes]
rs11169508	0.84[AFR][1000 genomes]
rs11169511	0.84[AFR][1000 genomes]
rs11169547	0.84[AFR][1000 genomes]
rs11169666	0.84[AFR][1000 genomes]
rs11169801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169908	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11609849	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11612004	0.84[AFR][1000 genomes]
rs11613205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12827647	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1554550	0.84[AFR][1000 genomes]
rs1601579	0.84[AFR][1000 genomes]
rs17464772	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17465893	0.87[CEU][hapmap]
rs17523988	1.00[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1843639	0.84[AFR][1000 genomes]
rs2056159	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2388060	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]
rs34204495	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36035670	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4332556	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6580755	0.84[AFR][1000 genomes]
rs7301104	0.84[AFR][1000 genomes]
rs7960621	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7967776	0.91[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7973992	0.84[AFR][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:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39203200-39276000	Weak transcription	Aorta	Aorta
2	chr12:39204000-39284800	Weak transcription	Lung	lung
3	chr12:39206600-39243800	Weak transcription	Left Ventricle	heart
4	chr12:39206600-39249200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:39206800-39241400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:39206800-39241400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:39216000-39237400	Weak transcription	Hela-S3	cervix
8	chr12:39219200-39242600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:39221800-39251800	Weak transcription	Liver	Liver
10	chr12:39223600-39238400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:39224000-39241800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:39227800-39237200	Weak transcription	GM12878-XiMat	blood
13	chr12:39229400-39252200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:39231800-39233200	Enhancers	Fetal Intestine Large	intestine
15	chr12:39231800-39233200	Enhancers	Fetal Intestine Small	intestine
16	chr12:39232000-39233200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr12:39232200-39239200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr12:39232400-39247600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:39232600-39233200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:39232800-39233200	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr12:39232800-39233200	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr12:39233000-39233200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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