Variant report

Variant	rs9364692
Chromosome Location	chr6:163956329-163956330
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:163956231..163958805-chr6:163964495..163966703,2	K562	blood:
2	chr6:163832850..163838270-chr6:163950827..163956360,5	K562	blood:

Variant related genes	Relation type
ENSG00000270419	Chromatin interaction
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1047935	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11962088	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs13199835	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13202282	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16895015	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1737328	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs17591955	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs2143358	0.83[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2294698	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294703	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2294706	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2294709	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35442073	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3756879	0.82[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs3763197	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs41268571	0.82[ASN][1000 genomes]
rs4263561	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs4708995	0.81[AFR][1000 genomes]
rs4709716	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4709717	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4709718	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4709720	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4709722	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6455897	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs6931903	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6939218	0.83[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs715020	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]
rs724826	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7758706	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs7772756	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs9346960	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9347760	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9364688	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9364689	1.00[ASW][hapmap];0.96[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];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9364691	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019551	chr6:163842358-163965216	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1017495	chr6:163856399-163981095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1027863	chr6:163934616-163965216	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	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
5	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
rs9364692	QKI	Cis_1M	lymphoblastoid	RTeQTL
rs9364692	SESTD1	trans	cerebellum	SCAN
rs9364692	LOC285796	cis	lymphoblastoid	seeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163926600-163991800	Weak transcription	Esophagus	oesophagus
2	chr6:163929800-163957000	Weak transcription	Primary B cells from cord blood	blood
3	chr6:163935200-163958800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr6:163935200-163959400	Weak transcription	Lung	lung
5	chr6:163936800-163957400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr6:163940200-163983000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:163944200-163957400	Enhancers	Brain Substantia Nigra	brain
8	chr6:163945000-163957400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:163948400-163958400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:163948600-163959000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:163948600-163964600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:163949000-163958000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr6:163949400-163959200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:163949600-163975200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:163949600-163992000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:163949600-163995400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:163951000-163978800	Weak transcription	Fetal Kidney	kidney
18	chr6:163951200-163993200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr6:163951600-163985800	Weak transcription	Hela-S3	cervix
20	chr6:163951800-163973400	Weak transcription	Fetal Stomach	stomach
21	chr6:163952000-163958600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:163952200-163957000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:163952400-163984400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr6:163952600-163958000	Weak transcription	Ovary	ovary
25	chr6:163952600-163958400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr6:163952600-163959200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:163952600-163959400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr6:163952600-163960200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:163952600-163960400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr6:163952600-163960800	Enhancers	Brain Cingulate Gyrus	brain
31	chr6:163952600-163961400	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr6:163952600-163972000	Weak transcription	Primary T cells from cord blood	blood
33	chr6:163952600-163979600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:163952600-163981400	Weak transcription	Pancreas	Pancrea
35	chr6:163952600-163982800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr6:163952600-163996600	Weak transcription	Gastric	stomach
37	chr6:163953000-163959600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr6:163953400-163958200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:163953800-163958800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:163953800-163964000	Weak transcription	Fetal Brain Male	brain
41	chr6:163954000-163957400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:163954000-163957400	Weak transcription	Placenta	Placenta
43	chr6:163954000-163958000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr6:163954000-163958000	Weak transcription	Psoas Muscle	Psoas
45	chr6:163954000-163958400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr6:163954000-163960200	Weak transcription	Spleen	Spleen
47	chr6:163954000-163968400	Weak transcription	K562	blood
48	chr6:163954000-163979400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:163954000-163984200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr6:163954000-163984400	Weak transcription	Aorta	Aorta

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