Variant report

Variant	rs11169879
Chromosome Location	chr12:39265829-39265830
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10506129	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10876086	0.84[AFR][1000 genomes]
rs10876149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10876163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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]
rs11169769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169908	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11609849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612004	0.84[AFR][1000 genomes]
rs11613205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11615668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12827647	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1554550	0.84[AFR][1000 genomes]
rs1601579	0.84[AFR][1000 genomes]
rs17464772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17523988	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1843639	0.84[AFR][1000 genomes]
rs2056159	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2388060	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34204495	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36035670	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4332556	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967776	0.86[EUR][1000 genomes];0.92[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:27 , 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	chr12:39238800-39271600	Weak transcription	NHEK	skin
4	chr12:39239200-39284000	Weak transcription	Hela-S3	cervix
5	chr12:39250600-39273200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:39252200-39276000	Weak transcription	Left Ventricle	heart
7	chr12:39252600-39272000	Weak transcription	A549	lung
8	chr12:39253000-39279600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:39253200-39272200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:39256800-39269400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:39257000-39271400	Weak transcription	HMEC	breast
12	chr12:39261800-39279600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr12:39263800-39277600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr12:39264000-39267000	Weak transcription	NHLF	lung
15	chr12:39264000-39272000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:39264800-39268400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr12:39265000-39266000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:39265000-39266000	Strong transcription	Liver	Liver
19	chr12:39265000-39266400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr12:39265000-39268800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:39265200-39266400	Enhancers	Primary hematopoietic stem cells	blood
22	chr12:39265200-39267600	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr12:39265600-39266000	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr12:39265600-39271600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:39265600-39272000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:39265600-39272200	Weak transcription	GM12878-XiMat	blood
27	chr12:39265800-39266800	Enhancers	Adipose Nuclei	Adipose

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