Variant report

Variant	rs10786018
Chromosome Location	chr10:93559751-93559752
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr10:93557289-93559806	IMR90	lung:	n/a	n/a
2	JUND	chr10:93559168-93559864	SK-N-SH	brain:	n/a	chr10:93559784-93559798 chr10:93559542-93559551 chr10:93559544-93559551 chr10:93559541-93559552
3	MXI1	chr10:93557578-93559858	SK-N-SH	brain:	n/a	n/a
4	STAT3	chr10:93558867-93560002	MCF10A-Er-Src	breast:	n/a	chr10:93559480-93559491 chr10:93559482-93559490 chr10:93559215-93559226
5	CHD1	chr10:93556973-93559802	IMR90	lung:	n/a	n/a
6	FOS	chr10:93559449-93559834	HUVEC	blood vessel:	n/a	chr10:93559784-93559798 chr10:93559542-93559551 chr10:93559544-93559551 chr10:93559541-93559552

No.	Distal block	Cell Line	Cell type
1	chr10:93558304..93560845-chr10:99161084..99163297,2	MCF-7	breast:
2	chr10:93558698..93560238-chr10:93571745..93574194,2	MCF-7	breast:
3	chr10:93422934..93425044-chr10:93558921..93560973,2	K562	blood:
4	chr10:93559267..93561929-chr10:93568041..93570595,2	MCF-7	breast:
5	chr10:93558185..93560569-chr10:93560780..93564031,3	MCF-7	breast:
6	chr10:93559330..93560916-chr10:93583898..93586021,2	MCF-7	breast:

Variant related genes	Relation type
TNKS2-AS1	TF binding region
ENSG00000052749	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10736064	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10748568	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786011	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10786013	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10786015	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10881934	1.00[JPT][hapmap]
rs10881959	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10881968	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11186695	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11186726	0.80[AMR][1000 genomes]
rs11186731	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11814405	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12248932	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12573311	0.84[ASN][1000 genomes]
rs1340420	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1539041	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs1572933	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1572934	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1770467	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1770470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1770472	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1770475	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1772180	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1772185	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1935030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935031	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2066276	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2259280	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2487513	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2487514	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2994394	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3930831	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4403720	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4933677	0.87[GIH][hapmap]
rs6583787	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7073486	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7077236	0.89[EUR][1000 genomes]
rs7085519	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7897784	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7911346	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918126	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs946896	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][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	esv3431124	chr10:93557397-93559945	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10786018	TNKS2-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs10786018	TNKS2-AS1	cis	Thyroid	GTEx
rs10786018	TNKS2-AS1	cis	Muscle Skeletal	GTEx
rs10786018	TNKS2-AS1	cis	Esophagus Mucosa	GTEx
rs10786018	TNKS2-AS1	cis	Adipose Subcutaneous	GTEx
rs10786018	PPP1R3C	cis	Esophagus Mucosa	GTEx
rs10786018	TNKS2-AS1	cis	Artery Tibial	GTEx
rs10786018	TNKS2-AS1	cis	Nerve Tibial	GTEx
rs10786018	TNKS2-AS1	cis	Esophagus Muscularis	GTEx
rs10786018	TNKS2-AS1	cis	Heart Left Ventricle	GTEx
rs10786018	TNKS2-AS1	cis	Artery Aorta	GTEx
rs10786018	TNKS2-AS1	cis	Stomach	GTEx
rs10786018	TNKS2-AS1	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93556000-93560000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr10:93556000-93560000	Active TSS	Aorta	Aorta
3	chr10:93556000-93560000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr10:93556000-93560200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr10:93556000-93560200	Active TSS	Stomach Smooth Muscle	stomach
6	chr10:93556000-93560800	Active TSS	Right Atrium	heart
7	chr10:93556000-93561200	Active TSS	Ovary	ovary
8	chr10:93556200-93559800	Active TSS	Fetal Stomach	stomach
9	chr10:93556200-93560000	Active TSS	Colonic Mucosa	Colon
10	chr10:93556200-93560200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr10:93556200-93560200	Active TSS	Right Ventricle	heart
12	chr10:93556200-93560800	Active TSS	Psoas Muscle	Psoas
13	chr10:93556200-93562000	Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr10:93556400-93559800	Active TSS	Primary T cells fromperipheralblood	blood
15	chr10:93556600-93560200	Active TSS	H9 Cell Line	embryonic stem cell
16	chr10:93556600-93560400	Active TSS	Fetal Muscle Trunk	muscle
17	chr10:93557000-93560200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr10:93557000-93560400	Active TSS	Placenta	Placenta
19	chr10:93557200-93559800	Active TSS	H1 Cell Line	embryonic stem cell
20	chr10:93557200-93559800	Active TSS	NHDF-Ad	bronchial
21	chr10:93557200-93560000	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr10:93557200-93560200	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr10:93557400-93559800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr10:93557400-93559800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr10:93557400-93559800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr10:93557400-93559800	Active TSS	Fetal Kidney	kidney
27	chr10:93557400-93559800	Active TSS	Fetal Lung	lung
28	chr10:93557400-93559800	Active TSS	Thymus	Thymus
29	chr10:93557400-93559800	Active TSS	HSMMtube	muscle
30	chr10:93557400-93560000	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr10:93557400-93560200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr10:93557400-93560400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr10:93557400-93560400	Active TSS	Fetal Muscle Leg	muscle
34	chr10:93557400-93560400	Active TSS	K562	blood
35	chr10:93557400-93560600	Active TSS	Fetal Intestine Large	intestine
36	chr10:93557600-93559800	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr10:93557600-93559800	Active TSS	Brain Substantia Nigra	brain
38	chr10:93557600-93559800	Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr10:93557600-93560000	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr10:93557600-93560000	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr10:93557600-93560000	Active TSS	Left Ventricle	heart
42	chr10:93557600-93560200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr10:93557800-93559800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr10:93557800-93559800	Active TSS	Fetal Intestine Small	intestine
45	chr10:93557800-93559800	Active TSS	NHLF	lung
46	chr10:93557800-93560000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr10:93557800-93560000	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr10:93557800-93560000	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr10:93557800-93560000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr10:93557800-93560000	Active TSS	Pancreatic Islets	Pancreatic Islet

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