Variant report

Variant	rs2840320
Chromosome Location	chr10:18434190-18434191
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10734038	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10740993	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10740995	0.96[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10740996	0.83[CEU][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10741003	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10764319	0.83[ASW][hapmap]
rs10764325	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10764326	0.88[CEU][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10764327	0.91[CEU][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10764329	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10764331	0.88[CEU][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10764332	0.88[CEU][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10828269	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10828277	0.95[CEU][hapmap];0.84[CHB][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10828280	0.88[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11596960	0.81[EUR][1000 genomes]
rs12572659	0.83[EUR][1000 genomes]
rs12770520	0.82[EUR][1000 genomes]
rs1331330	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2183718	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2183719	0.89[YRI][hapmap]
rs2357790	0.83[EUR][1000 genomes]
rs7080195	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7100500	0.82[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054616	chr10:18433954-18451969	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2840320	PTPLA	cis	cerebellum	SCAN
rs2840320	CACNB2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18430600-18446400	Weak transcription	Brain Angular Gyrus	brain
2	chr10:18430800-18434800	Weak transcription	Left Ventricle	heart
3	chr10:18430800-18442400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr10:18431000-18440600	Weak transcription	Fetal Intestine Small	intestine
5	chr10:18431200-18434600	Weak transcription	Brain Hippocampus Middle	brain
6	chr10:18431200-18437400	Weak transcription	Fetal Stomach	stomach
7	chr10:18431200-18440600	Weak transcription	Aorta	Aorta
8	chr10:18431200-18447800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr10:18431200-18447800	Weak transcription	Fetal Intestine Large	intestine
10	chr10:18431400-18437600	Weak transcription	Right Ventricle	heart
11	chr10:18431400-18440600	Weak transcription	Ovary	ovary
12	chr10:18431400-18441200	Enhancers	Rectal Smooth Muscle	rectum
13	chr10:18431400-18468800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr10:18432200-18435200	Enhancers	Fetal Heart	heart
15	chr10:18432400-18434400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr10:18432400-18440000	Weak transcription	Fetal Brain Male	brain
17	chr10:18432600-18446800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr10:18432600-18448000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr10:18432800-18434600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:18433200-18435400	Enhancers	Colon Smooth Muscle	Colon
21	chr10:18433600-18434200	Enhancers	Primary hematopoietic stem cells	blood
22	chr10:18433600-18434800	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr10:18433600-18436000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr10:18433800-18434200	Enhancers	Pancreas	Pancrea
25	chr10:18433800-18435000	Enhancers	Brain Anterior Caudate	brain
26	chr10:18433800-18435200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr10:18433800-18435400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr10:18433800-18435400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr10:18433800-18435400	Enhancers	Fetal Lung	lung
30	chr10:18434000-18434200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr10:18434000-18434400	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr10:18434000-18434800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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