Variant report

Variant	rs1539246
Chromosome Location	chr10:93371754-93371755
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:93348429..93351278-chr10:93370659..93373317,2	K562	blood:
2	chr10:93349778..93351711-chr10:93371480..93373317,2	K562	blood:
3	chr10:93367612..93370294-chr10:93370474..93375742,6	K562	blood:
4	chr10:93362637..93365388-chr10:93371389..93374177,2	MCF-7	breast:
5	chr10:93371223..93372891-chr10:93374209..93376452,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10509629	0.81[CHB][hapmap]
rs10732773	0.91[EUR][1000 genomes]
rs10748563	0.86[EUR][1000 genomes]
rs10786008	0.94[EUR][1000 genomes]
rs10881929	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10881934	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs10881935	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10881938	0.87[EUR][1000 genomes]
rs10881939	0.94[EUR][1000 genomes]
rs10881940	0.93[EUR][1000 genomes]
rs10881941	0.88[EUR][1000 genomes]
rs10881942	0.93[EUR][1000 genomes]
rs10881943	0.93[EUR][1000 genomes]
rs10881945	0.91[EUR][1000 genomes]
rs11186626	0.81[AMR][1000 genomes]
rs11186640	0.93[EUR][1000 genomes]
rs1891271	0.90[EUR][1000 genomes]
rs1891272	0.91[EUR][1000 genomes]
rs1970506	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs2000177	0.94[EUR][1000 genomes]
rs2000178	0.94[EUR][1000 genomes]
rs2027486	0.94[EUR][1000 genomes]
rs2421621	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2421623	0.94[EUR][1000 genomes]
rs2421624	0.91[EUR][1000 genomes]
rs2421625	0.91[EUR][1000 genomes]
rs2421626	0.91[EUR][1000 genomes]
rs2421627	0.91[EUR][1000 genomes]
rs2421628	0.91[EUR][1000 genomes]
rs2421629	0.91[EUR][1000 genomes]
rs4439432	0.91[EUR][1000 genomes]
rs4933216	0.91[EUR][1000 genomes]
rs4933677	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4933681	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4933682	0.90[EUR][1000 genomes]
rs4933683	0.94[EUR][1000 genomes]
rs4933684	0.90[EUR][1000 genomes]
rs4933685	0.87[EUR][1000 genomes]
rs4933687	0.94[EUR][1000 genomes]
rs4933690	0.91[EUR][1000 genomes]
rs4933691	0.91[EUR][1000 genomes]
rs4933692	0.91[EUR][1000 genomes]
rs6583782	0.91[EUR][1000 genomes]
rs7071844	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7077656	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7084386	0.89[EUR][1000 genomes]
rs7087959	0.90[EUR][1000 genomes]
rs7088831	0.94[EUR][1000 genomes]
rs7897524	0.94[EUR][1000 genomes]
rs7900799	0.88[EUR][1000 genomes]
rs7900863	0.91[EUR][1000 genomes]
rs7908980	0.90[EUR][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	nsv551914	chr10:93365015-93384073	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1539246	TNKS2-AS1	cis	Heart Left Ventricle	GTEx
rs1539246	TNKS2-AS1	cis	Esophagus Muscularis	GTEx
rs1539246	TNKS2-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs1539246	TNKS2-AS1	cis	Muscle Skeletal	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93365600-93373000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:93367400-93372000	Enhancers	NHLF	lung
3	chr10:93367400-93373600	Enhancers	NHDF-Ad	bronchial
4	chr10:93368000-93388600	Weak transcription	Brain Angular Gyrus	brain
5	chr10:93368800-93372800	Enhancers	Muscle Satellite Cultured Cells	--
6	chr10:93368800-93373000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr10:93368800-93373200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr10:93368800-93373600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr10:93368800-93373800	Weak transcription	Small Intestine	intestine
10	chr10:93369000-93371800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr10:93369000-93371800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr10:93369000-93371800	Enhancers	Rectal Smooth Muscle	rectum
13	chr10:93369000-93372000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr10:93369000-93372800	Weak transcription	HUVEC	blood vessel
15	chr10:93369000-93373200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr10:93369000-93387600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr10:93369200-93372000	Enhancers	Colon Smooth Muscle	Colon
18	chr10:93369200-93373200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr10:93369200-93373600	Weak transcription	Colonic Mucosa	Colon
20	chr10:93369400-93371800	Enhancers	Stomach Smooth Muscle	stomach
21	chr10:93369400-93371800	Enhancers	K562	blood
22	chr10:93369400-93372800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr10:93369400-93373000	Enhancers	Hela-S3	cervix
24	chr10:93369400-93373600	Weak transcription	Adipose Nuclei	Adipose
25	chr10:93369400-93378600	Weak transcription	Fetal Intestine Small	intestine
26	chr10:93369400-93379200	Weak transcription	Liver	Liver
27	chr10:93369600-93373000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr10:93369600-93387800	Weak transcription	Fetal Brain Male	brain
29	chr10:93369800-93373000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr10:93369800-93373400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr10:93370000-93371800	Enhancers	Fetal Lung	lung
32	chr10:93370400-93374200	Enhancers	Fetal Heart	heart
33	chr10:93370600-93371800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr10:93370600-93371800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr10:93370800-93371800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr10:93371000-93371800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr10:93371000-93372600	Weak transcription	NH-A	brain
38	chr10:93371000-93372800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr10:93371000-93373000	Weak transcription	HMEC	breast
40	chr10:93371000-93373200	Weak transcription	NHEK	skin
41	chr10:93371000-93373400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr10:93371200-93372600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr10:93371200-93376800	Weak transcription	Spleen	Spleen
44	chr10:93371400-93372400	Weak transcription	HSMM	muscle
45	chr10:93371400-93372600	Weak transcription	HSMMtube	muscle
46	chr10:93371400-93372600	Weak transcription	Osteobl	bone
47	chr10:93371400-93373000	Weak transcription	Left Ventricle	heart
48	chr10:93371400-93373000	Weak transcription	A549	lung
49	chr10:93371400-93373200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr10:93371400-93373200	Weak transcription	Aorta	Aorta

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