Variant report

Variant	rs1539041
Chromosome Location	chr10:93577141-93577142
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:93576673..93578768-chr10:93627898..93630166,2	MCF-7	breast:
2	chr10:93556969..93558675-chr10:93576567..93578555,2	MCF-7	breast:
3	chr10:93561483..93563173-chr10:93576310..93578426,2	K562	blood:

Variant related genes	Relation type
ENSG00000228701	Chromatin interaction
ENSG00000107854	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10736064	0.85[ASN][1000 genomes]
rs10748568	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]
rs10748569	1.00[ASN][1000 genomes]
rs10786011	0.81[ASN][1000 genomes]
rs10786013	0.81[ASN][1000 genomes]
rs10786015	0.91[ASN][1000 genomes]
rs10786018	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]
rs1080495	0.85[EUR][1000 genomes]
rs10881934	1.00[JPT][hapmap]
rs10881959	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[ASN][1000 genomes]
rs11186695	1.00[ASN][1000 genomes]
rs11814405	0.87[ASN][1000 genomes]
rs12248932	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12573311	0.84[ASN][1000 genomes]
rs1340420	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs1572933	0.87[ASN][1000 genomes]
rs1572934	0.87[ASN][1000 genomes]
rs1770467	0.83[ASN][1000 genomes]
rs1770470	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs1770472	0.83[ASN][1000 genomes]
rs1772180	0.83[ASN][1000 genomes]
rs1772185	0.83[ASN][1000 genomes]
rs1935030	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2066276	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]
rs2421737	0.85[EUR][1000 genomes]
rs3930831	0.81[ASN][1000 genomes]
rs4403720	0.91[ASN][1000 genomes]
rs6583787	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs7073486	0.81[ASN][1000 genomes]
rs7085519	1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs7897784	0.81[ASN][1000 genomes]
rs7911346	1.00[ASN][1000 genomes]
rs7918126	0.81[ASN][1000 genomes]
rs946896	0.83[ASN][1000 genomes]

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1539041	RBP4	cis	parietal	SCAN
rs1539041	TNKS2-AS1	cis	Adipose Subcutaneous	GTEx
rs1539041	TNKS2-AS1	cis	Stomach	GTEx
rs1539041	TNKS2-AS1	cis	Artery Tibial	GTEx
rs1539041	TNKS2-AS1	cis	Thyroid	GTEx
rs1539041	TNKS2-AS1	cis	Esophagus Mucosa	GTEx
rs1539041	PPP1R3C	cis	Esophagus Mucosa	GTEx
rs1539041	TNKS2-AS1	cis	Heart Left Ventricle	GTEx
rs1539041	TNKS2-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs1539041	TNKS2-AS1	cis	Muscle Skeletal	GTEx
rs1539041	TNKS2-AS1	cis	lung	GTEx
rs1539041	TNKS2-AS1	cis	Esophagus Muscularis	GTEx
rs1539041	SLC16A12	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93559000-93580800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:93559600-93578800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr10:93559600-93599200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:93560200-93577600	Weak transcription	Colonic Mucosa	Colon
5	chr10:93560200-93589400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr10:93563400-93580800	Weak transcription	Fetal Stomach	stomach
7	chr10:93563600-93578200	Weak transcription	Aorta	Aorta
8	chr10:93563800-93579400	Weak transcription	Right Atrium	heart
9	chr10:93564000-93579000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr10:93565800-93577800	Weak transcription	Right Ventricle	heart
11	chr10:93565800-93578200	Weak transcription	Gastric	stomach
12	chr10:93565800-93578400	Weak transcription	Brain Angular Gyrus	brain
13	chr10:93565800-93579800	Weak transcription	Small Intestine	intestine
14	chr10:93567200-93624200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr10:93567600-93579800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr10:93569200-93626800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr10:93570000-93608000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr10:93570800-93625000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr10:93570800-93626000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr10:93570800-93626000	Strong transcription	Dnd41	blood
21	chr10:93571000-93580800	Weak transcription	Fetal Intestine Small	intestine
22	chr10:93571000-93623200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr10:93571000-93624000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr10:93571000-93625800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr10:93571200-93578400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr10:93571200-93580000	Weak transcription	Pancreas	Pancrea
27	chr10:93571200-93626400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr10:93571400-93592800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr10:93571400-93626400	Strong transcription	Liver	Liver
30	chr10:93571400-93626400	Strong transcription	Fetal Thymus	thymus
31	chr10:93571600-93581400	Weak transcription	Spleen	Spleen
32	chr10:93572000-93579200	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr10:93572000-93589600	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr10:93572000-93626200	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr10:93572000-93626400	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr10:93572000-93626400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr10:93572200-93591000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr10:93572200-93623600	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr10:93572200-93625600	Strong transcription	Placenta	Placenta
40	chr10:93572200-93626400	Strong transcription	Primary B cells from cord blood	blood
41	chr10:93572400-93581600	Strong transcription	Hela-S3	cervix
42	chr10:93572400-93582400	Strong transcription	Primary hematopoietic stem cells	blood
43	chr10:93572400-93584200	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr10:93572400-93584400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr10:93572400-93595200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr10:93572400-93623000	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr10:93572400-93624400	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr10:93572400-93624800	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr10:93572400-93626000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr10:93572400-93626000	Strong transcription	Primary B cells from peripheral blood	blood

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