Variant report

Variant	rs12682981
Chromosome Location	chr9:86465369-86465370
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10114889	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap]
rs10868071	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10868076	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11140251	0.88[CHB][hapmap]
rs11140253	0.88[CHB][hapmap]
rs11140265	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs11140304	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12378956	0.94[CHB][hapmap]
rs13290882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs13296528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs167203	0.83[CEU][hapmap]
rs1831757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs1982151	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2378661	0.94[CHB][hapmap]
rs2576362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs2780103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs295273	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs296886	0.82[CEU][hapmap]
rs296887	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs296888	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs296889	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs296890	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs296893	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3119921	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3180887	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs3818725	0.88[CHB][hapmap]
rs4147132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4147133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs418816	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs419250	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4535826	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6559751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs7020300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs7033292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs7047907	0.94[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap]
rs7853377	0.83[CEU][hapmap]
rs7869321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9410887	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9410888	0.88[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs963459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469859	chr9:86398152-86587957	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv482641	chr9:86398152-86587957	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv982312	chr9:86424154-86490046	Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv6590	chr9:86435603-86480442	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv8540	chr9:86458587-86470369	Strong transcription ZNF genes & repeats Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12682981	GKAP1	cis	multi-tissue	Pritchard

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86447800-86470800	Weak transcription	Brain Germinal Matrix	brain
2	chr9:86452000-86467800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:86456200-86466200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:86456600-86472600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr9:86457400-86468400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr9:86457400-86469000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr9:86459800-86466400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:86460000-86474000	Weak transcription	Adipose Nuclei	Adipose
9	chr9:86460400-86465400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr9:86460600-86465400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:86460600-86518200	Weak transcription	Thymus	Thymus
12	chr9:86461600-86535400	Weak transcription	Fetal Intestine Small	intestine
13	chr9:86461600-86535400	Weak transcription	Ovary	ovary
14	chr9:86462200-86466400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr9:86462200-86471200	Weak transcription	Liver	Liver
16	chr9:86462200-86475400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:86462200-86535200	Weak transcription	Fetal Brain Female	brain
18	chr9:86462400-86482400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:86462600-86468600	Weak transcription	Primary T cells from cord blood	blood
20	chr9:86462600-86469600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:86462600-86499200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr9:86462600-86500600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:86462600-86503800	Weak transcription	Dnd41	blood
24	chr9:86462600-86535200	Weak transcription	Brain Anterior Caudate	brain
25	chr9:86462800-86465400	Weak transcription	Fetal Thymus	thymus
26	chr9:86462800-86468600	Weak transcription	Placenta	Placenta
27	chr9:86462800-86471200	Weak transcription	Fetal Lung	lung
28	chr9:86462800-86515000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:86462800-86518000	Weak transcription	Fetal Intestine Large	intestine
30	chr9:86462800-86518000	Weak transcription	Fetal Stomach	stomach

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