Variant report

Variant	rs7978838
Chromosome Location	chr12:39288066-39288067
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10160990	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10732735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1095573	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs11169615	0.85[EUR][1000 genomes]
rs11169618	0.85[EUR][1000 genomes]
rs11537523	0.85[EUR][1000 genomes]
rs1356267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1400281	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1516553	0.90[EUR][1000 genomes]
rs1516557	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1533918	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs1607040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1615648	0.82[CEU][hapmap];0.90[JPT][hapmap]
rs1684426	0.81[EUR][1000 genomes]
rs1719833	0.82[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs1719847	0.82[CEU][hapmap];0.90[JPT][hapmap]
rs1719860	0.82[EUR][1000 genomes]
rs1878225	0.81[JPT][hapmap]
rs1914052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1996879	0.88[EUR][1000 genomes]
rs2056529	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2069210	0.82[CEU][hapmap];0.90[JPT][hapmap]
rs4002228	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4768394	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7298168	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7974247	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs826849	0.82[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs826853	0.90[JPT][hapmap]
rs826860	0.90[JPT][hapmap]
rs826861	0.82[CEU][hapmap];0.90[JPT][hapmap]
rs826862	0.82[CEU][hapmap];0.90[JPT][hapmap]
rs826869	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs826872	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs826884	0.85[EUR][1000 genomes]
rs826885	0.83[EUR][1000 genomes]
rs826887	0.90[JPT][hapmap]
rs826890	0.94[JPT][hapmap]
rs826894	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs851933	0.89[JPT][hapmap]
rs862331	0.90[JPT][hapmap]
rs862332	0.85[EUR][1000 genomes]
rs866120	0.90[JPT][hapmap]
rs908511	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv899009	chr12:39284077-39441096	Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39271800-39297200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:39284200-39289600	Weak transcription	Adipose Nuclei	Adipose
3	chr12:39284600-39289200	Weak transcription	HUVEC	blood vessel
4	chr12:39284800-39288800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:39285000-39291800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:39285000-39296400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:39285800-39288600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:39286000-39294600	Weak transcription	Lung	lung
9	chr12:39286200-39291800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:39286200-39291800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:39286200-39291800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr12:39286400-39288200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:39286400-39289400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:39286400-39290000	Weak transcription	NHEK	skin
15	chr12:39286400-39290200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:39286400-39290200	Weak transcription	Right Atrium	heart
17	chr12:39286400-39290200	Weak transcription	HMEC	breast
18	chr12:39286400-39293600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:39286600-39288600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:39286600-39290400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:39286600-39297400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr12:39287000-39288200	Weak transcription	GM12878-XiMat	blood
23	chr12:39287200-39290000	Weak transcription	Colon Smooth Muscle	Colon
24	chr12:39287200-39291800	Weak transcription	A549	lung
25	chr12:39287400-39288400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:39287400-39290000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:39287400-39290400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr12:39287400-39291600	Weak transcription	Placenta	Placenta
29	chr12:39287400-39291800	Weak transcription	Hela-S3	cervix
30	chr12:39287400-39296400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:39287400-39298600	Weak transcription	Aorta	Aorta
32	chr12:39288000-39296600	Weak transcription	Liver	Liver

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