Variant report

Variant	rs10787540
Chromosome Location	chr10:116364424-116364425
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10787539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10787541	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196800	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11196802	0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11196806	0.92[JPT][hapmap]
rs11196810	0.92[JPT][hapmap]
rs11196825	0.91[JPT][hapmap]
rs11196826	0.92[JPT][hapmap]
rs11196841	0.92[JPT][hapmap]
rs11196844	0.83[JPT][hapmap]
rs11196845	0.83[JPT][hapmap]
rs11196853	0.83[JPT][hapmap]
rs11196854	0.83[JPT][hapmap]
rs11196861	0.83[JPT][hapmap]
rs12146316	0.86[JPT][hapmap]
rs12768716	0.83[JPT][hapmap]
rs17719647	0.92[JPT][hapmap]
rs2483591	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4752039	0.92[JPT][hapmap]
rs4752071	0.92[JPT][hapmap]
rs4752089	0.83[JPT][hapmap]
rs7080854	0.90[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7094673	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs71484950	0.95[ASN][1000 genomes]
rs955634	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10787540	SLC18A2	cis	parietal	SCAN
rs10787540	SHOC2	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116345000-116382400	Weak transcription	HSMM	muscle
2	chr10:116352600-116367600	Weak transcription	Ovary	ovary
3	chr10:116353200-116364600	Weak transcription	Brain Hippocampus Middle	brain
4	chr10:116354600-116364600	Weak transcription	Gastric	stomach
5	chr10:116354800-116378600	Weak transcription	Fetal Stomach	stomach
6	chr10:116355400-116371000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr10:116357600-116364600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr10:116357600-116365600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr10:116358600-116364600	Weak transcription	Aorta	Aorta
10	chr10:116359200-116366600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr10:116360600-116364600	Weak transcription	Right Atrium	heart
12	chr10:116360600-116365400	Weak transcription	Esophagus	oesophagus
13	chr10:116360600-116370600	Weak transcription	Lung	lung
14	chr10:116360600-116380600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr10:116361200-116364800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr10:116361400-116379000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr10:116361600-116365400	Weak transcription	Fetal Intestine Small	intestine
18	chr10:116361600-116378200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr10:116361800-116365200	Weak transcription	Pancreas	Pancrea
20	chr10:116361800-116365600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr10:116362400-116364600	Weak transcription	Liver	Liver
22	chr10:116362400-116366000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr10:116362600-116365400	Enhancers	Brain Angular Gyrus	brain
24	chr10:116362600-116365600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr10:116362600-116365800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr10:116362600-116367600	Enhancers	Stomach Mucosa	stomach
27	chr10:116362800-116364600	Enhancers	A549	lung
28	chr10:116362800-116365600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr10:116362800-116365800	Enhancers	Brain Anterior Caudate	brain
30	chr10:116362800-116365800	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr10:116363000-116365200	Weak transcription	Fetal Intestine Large	intestine
32	chr10:116363000-116365400	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr10:116363000-116366000	Enhancers	HepG2	liver
34	chr10:116363200-116364600	Weak transcription	Right Ventricle	heart
35	chr10:116363200-116364800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr10:116363600-116366000	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr10:116363800-116364600	Enhancers	Colon Smooth Muscle	Colon
38	chr10:116363800-116364600	Enhancers	Fetal Lung	lung
39	chr10:116363800-116365000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr10:116363800-116365000	Enhancers	HUVEC	blood vessel
41	chr10:116363800-116365200	Enhancers	Duodenum Mucosa	Duodenum
42	chr10:116363800-116365600	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr10:116363800-116365600	Enhancers	HSMMtube	muscle
44	chr10:116363800-116365800	Enhancers	Hela-S3	cervix
45	chr10:116364000-116365600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr10:116364000-116365600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr10:116364000-116365600	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr10:116364000-116365800	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr10:116364000-116366600	Enhancers	Fetal Kidney	kidney
50	chr10:116364000-116368200	Enhancers	Adipose Nuclei	Adipose

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