Variant report

Variant	rs11186722
Chromosome Location	chr10:93643371-93643372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:93642306..93644379-chr10:93658449..93661429,2	MCF-7	breast:
2	chr10:93638890..93643512-chr10:93665882..93670219,9	MCF-7	breast:
3	chr10:93643244..93645164-chr10:93648326..93650268,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272817	Chromatin interaction
ENSG00000174721	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10509634	0.80[JPT][hapmap]
rs10881966	0.80[JPT][hapmap]
rs10881967	0.80[JPT][hapmap]
rs10881973	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10881974	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10881978	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10881979	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10881987	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10881988	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11186696	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11186719	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11186721	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11186723	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12253245	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1539042	0.90[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1592050	0.80[JPT][hapmap]
rs1770466	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1770476	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1772179	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1772182	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1772183	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1772189	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1890896	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2153655	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2259305	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2994393	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802650	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4611111	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4612711	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4933698	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7069232	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7076687	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7079479	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7085519	0.80[LWK][hapmap]
rs7096581	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7917858	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv7491	chr10:93626192-93671694	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv1842657	chr10:93634155-93668663	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11186722	TNKS2-AS1	cis	Thyroid	GTEx
rs11186722	IFIT3	cis	parietal	SCAN
rs11186722	TNKS2-AS1	cis	Heart Left Ventricle	GTEx
rs11186722	TNKS2-AS1	cis	Esophagus Mucosa	GTEx
rs11186722	TNKS2-AS1	cis	Adipose Subcutaneous	GTEx
rs11186722	TNKS2-AS1	cis	lung	GTEx
rs11186722	TNKS2-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs11186722	TNKS2-AS1	cis	Artery Tibial	GTEx
rs11186722	TNKS2-AS1	cis	Muscle Skeletal	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93608800-93643400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:93639800-93643400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:93640200-93643400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr10:93640400-93643400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr10:93640400-93643400	Weak transcription	Brain Substantia Nigra	brain
6	chr10:93640600-93644800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr10:93640800-93643400	Weak transcription	HMEC	breast
8	chr10:93641000-93643400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr10:93642600-93645000	Enhancers	Placenta	Placenta
10	chr10:93642800-93643400	Enhancers	Fetal Muscle Trunk	muscle
11	chr10:93643000-93643400	Enhancers	H1 Cell Line	embryonic stem cell
12	chr10:93643000-93643400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr10:93643000-93643400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr10:93643000-93643400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr10:93643000-93643400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr10:93643000-93643400	Enhancers	Fetal Brain Female	brain
17	chr10:93643000-93643400	Enhancers	Fetal Heart	heart
18	chr10:93643000-93643400	Enhancers	Fetal Lung	lung
19	chr10:93643000-93643400	Enhancers	Fetal Muscle Leg	muscle
20	chr10:93643000-93643400	Enhancers	NHDF-Ad	bronchial
21	chr10:93643000-93643600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr10:93643000-93644200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr10:93643000-93644200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr10:93643000-93644200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr10:93643000-93644200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr10:93643000-93644600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr10:93643000-93645600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr10:93643000-93645800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr10:93643000-93645800	Enhancers	Fetal Brain Male	brain
30	chr10:93643200-93643400	Enhancers	H9 Cell Line	embryonic stem cell
31	chr10:93643200-93643400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr10:93643200-93643400	Enhancers	Brain Cingulate Gyrus	brain
33	chr10:93643200-93643400	Enhancers	Brain Germinal Matrix	brain
34	chr10:93643200-93643400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr10:93643200-93643400	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
36	chr10:93643200-93643400	Enhancers	Right Ventricle	heart
37	chr10:93643200-93643600	Active TSS	Brain Anterior Caudate	brain
38	chr10:93643200-93643600	Active TSS	Brain Hippocampus Middle	brain
39	chr10:93643200-93643600	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr10:93643200-93643600	Enhancers	Esophagus	oesophagus
41	chr10:93643200-93643600	Flanking Active TSS	Psoas Muscle	Psoas
42	chr10:93643200-93643600	Flanking Active TSS	Right Atrium	heart
43	chr10:93643200-93643800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr10:93643200-93643800	Active TSS	Aorta	Aorta
45	chr10:93643200-93643800	Enhancers	Brain Angular Gyrus	brain
46	chr10:93643200-93643800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
47	chr10:93643200-93643800	Flanking Active TSS	Fetal Kidney	kidney
48	chr10:93643200-93643800	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr10:93643200-93643800	Enhancers	Lung	lung
50	chr10:93643200-93643800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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