Variant report

Variant	rs2483568
Chromosome Location	chr10:116333411-116333412
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11196778	0.86[EUR][1000 genomes]
rs12413487	0.86[CEU][hapmap];0.97[EUR][1000 genomes]
rs2483535	0.86[TSI][hapmap]
rs2483538	0.97[EUR][1000 genomes]
rs2483539	0.86[TSI][hapmap]
rs2483541	0.86[TSI][hapmap]
rs2483548	0.86[TSI][hapmap]
rs2483549	0.93[CEU][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs2483552	0.83[TSI][hapmap]
rs2483553	0.86[TSI][hapmap]
rs2483560	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2483563	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483573	0.84[AMR][1000 genomes]
rs2483578	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483581	0.80[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483583	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2483590	0.87[EUR][1000 genomes]
rs2497663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2497730	0.86[TSI][hapmap]
rs2497731	0.86[TSI][hapmap]
rs2497733	0.93[CEU][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs2497743	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2497747	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497748	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497749	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4128920	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs4998667	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58938015	0.97[EUR][1000 genomes]
rs60588618	0.87[EUR][1000 genomes]
rs72826986	0.87[EUR][1000 genomes]
rs72826987	0.86[EUR][1000 genomes]
rs72829115	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7913199	0.86[CEU][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs7915301	0.86[AMR][1000 genomes]
rs9421186	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9421190	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs985273	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2483568	ABLIM1	cis	multi-tissue	Pritchard

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116311600-116336600	Weak transcription	Colonic Mucosa	Colon
2	chr10:116312000-116334600	Weak transcription	Esophagus	oesophagus
3	chr10:116312000-116335000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr10:116312000-116335200	Weak transcription	Pancreas	Pancrea
5	chr10:116318000-116335200	Weak transcription	Psoas Muscle	Psoas
6	chr10:116318000-116337200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr10:116318400-116336600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr10:116320400-116334000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr10:116321400-116336600	Weak transcription	Fetal Lung	lung
10	chr10:116323000-116334600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr10:116323000-116336000	Weak transcription	Lung	lung
12	chr10:116323400-116352000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr10:116323800-116352000	Weak transcription	Fetal Intestine Large	intestine
14	chr10:116324200-116337400	Weak transcription	Fetal Stomach	stomach
15	chr10:116324800-116334600	Weak transcription	HUVEC	blood vessel
16	chr10:116325000-116334400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr10:116325200-116335200	Weak transcription	Brain Angular Gyrus	brain
18	chr10:116325400-116335200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr10:116325400-116335600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr10:116325600-116336000	Weak transcription	Fetal Muscle Leg	muscle
21	chr10:116327000-116334600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr10:116328000-116334200	Weak transcription	Thymus	Thymus
23	chr10:116330200-116335200	Weak transcription	HSMM	muscle
24	chr10:116330400-116336000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr10:116331000-116339000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr10:116331200-116333600	Enhancers	Fetal Heart	heart
27	chr10:116331200-116334600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr10:116331400-116334600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr10:116331400-116335400	Weak transcription	NHEK	skin
30	chr10:116331400-116336000	Weak transcription	Brain Anterior Caudate	brain
31	chr10:116331400-116336000	Weak transcription	Ovary	ovary
32	chr10:116331600-116334600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr10:116331600-116334600	Weak transcription	Right Ventricle	heart
34	chr10:116331600-116334600	Weak transcription	HSMMtube	muscle
35	chr10:116331600-116335000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr10:116331600-116335000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr10:116331600-116335200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr10:116331600-116335200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr10:116331600-116335200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr10:116331600-116335800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr10:116331800-116335400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr10:116331800-116335400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr10:116331800-116335400	Weak transcription	Aorta	Aorta
44	chr10:116331800-116336000	Weak transcription	NH-A	brain
45	chr10:116332000-116335200	Weak transcription	Adipose Nuclei	Adipose
46	chr10:116332200-116334600	Enhancers	Liver	Liver
47	chr10:116332200-116337000	Weak transcription	A549	lung
48	chr10:116332400-116334400	Weak transcription	Fetal Intestine Small	intestine
49	chr10:116332600-116333600	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr10:116332600-116335200	Weak transcription	Rectal Smooth Muscle	rectum

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