Variant report

Variant	rs715020
Chromosome Location	chr6:163986482-163986483
allele	C/T
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	POLR2A	chr6:163985258-163986650	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:163976834..163978831-chr6:163984361..163986951,2	K562	blood:
2	chr6:163834433..163837014-chr6:163986395..163988827,2	K562	blood:
3	chr6:163836144..163840696-chr6:163983068..163987938,4	K562	blood:

Variant related genes	Relation type
QKI	TF binding region
ENSG00000270419	Chromatin interaction
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1047935	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11962088	0.84[JPT][hapmap]
rs13199835	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13202282	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16895015	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1737328	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs17591955	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2143358	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2294698	0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2294703	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2294706	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294709	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35442073	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3756879	0.88[CHB][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs3763197	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs41268571	0.85[ASN][1000 genomes]
rs4263561	0.89[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs4709716	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4709717	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4709718	0.88[EUR][1000 genomes]
rs4709720	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4709722	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6455897	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs6931903	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6939218	0.85[CHD][hapmap];0.90[JPT][hapmap]
rs724826	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7758706	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs7772756	1.00[JPT][hapmap]
rs9346960	0.84[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9347760	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9364688	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9364689	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9364691	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9364692	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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	nsv1018860	chr6:163939347-164532579	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538526	chr6:163939347-164532579	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs715020	LOC285796	cis	lymphoblastoid	seeQTL
rs715020	QKI	Cis_1M	lymphoblastoid	RTeQTL
rs715020	SESTD1	trans	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163926600-163991800	Weak transcription	Esophagus	oesophagus
2	chr6:163949600-163992000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:163949600-163995400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:163951200-163993200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:163952600-163996600	Weak transcription	Gastric	stomach
6	chr6:163954000-163991600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:163958200-163991600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:163959800-163997200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:163960600-163993000	Weak transcription	A549	lung
10	chr6:163965600-163995000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:163966800-163987000	Weak transcription	Colon Smooth Muscle	Colon
12	chr6:163968800-163991800	Weak transcription	Fetal Brain Male	brain
13	chr6:163969000-163991800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:163970400-163991600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:163970800-164000200	Weak transcription	Right Atrium	heart
16	chr6:163972600-163995600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr6:163974000-163997000	Weak transcription	Fetal Intestine Small	intestine
18	chr6:163974200-163997000	Weak transcription	Fetal Intestine Large	intestine
19	chr6:163976000-163993200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr6:163977000-163993000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr6:163978000-163998000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr6:163978400-163989800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:163978800-163997600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr6:163979200-163996200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:163979400-163987600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:163979400-163989200	Strong transcription	HepG2	liver
27	chr6:163979800-163989200	Genic enhancers	Brain Substantia Nigra	brain
28	chr6:163979800-163990600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:163980000-163988000	Genic enhancers	Brain Anterior Caudate	brain
30	chr6:163980000-163991600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr6:163980000-163991600	Weak transcription	Thymus	Thymus
32	chr6:163980000-163997200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr6:163980200-163991600	Weak transcription	Lung	lung
34	chr6:163980200-163996000	Weak transcription	Small Intestine	intestine
35	chr6:163980400-163991600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:163982600-163994000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:163982800-163987800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:163982800-163988000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr6:163982800-163988000	Genic enhancers	Brain Cingulate Gyrus	brain
40	chr6:163982800-163988000	Strong transcription	GM12878-XiMat	blood
41	chr6:163982800-163988000	Strong transcription	K562	blood
42	chr6:163982800-163988400	Strong transcription	NHDF-Ad	bronchial
43	chr6:163982800-163989200	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr6:163982800-163989200	Strong transcription	Primary B cells from peripheral blood	blood
45	chr6:163982800-163989200	Strong transcription	Placenta	Placenta
46	chr6:163982800-163989600	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:163982800-163996800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr6:163982800-163998000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr6:163983000-163987800	Strong transcription	HUVEC	blood vessel
50	chr6:163983000-163988000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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