Variant report

Variant	rs9347760
Chromosome Location	chr6:163954572-163954573
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	FOXA1	chr6:163954439-163954840	A549	lung:	n/a	n/a
2	JUND	chr6:163954411-163954974	SK-N-SH	brain:	n/a	chr6:163954754-163954764 chr6:163954754-163954764 chr6:163954756-163954767 chr6:163954754-163954764 chr6:163954754-163954764
3	GATA3	chr6:163954331-163954982	SK-N-SH	brain:	n/a	n/a
4	KAP1	chr6:163954523-163954979	U2OS	brain:	n/a	n/a
5	NR3C1	chr6:163954498-163954849	A549	lung:	n/a	chr6:163954755-163954764
6	JUND	chr6:163954397-163955039	SK-N-SH	brain:	n/a	chr6:163954754-163954764 chr6:163954754-163954764 chr6:163954756-163954767 chr6:163954754-163954764 chr6:163954754-163954764
7	FOS	chr6:163954467-163954898	MCF10A-Er-Src	breast:	n/a	chr6:163954754-163954764 chr6:163954754-163954764 chr6:163954756-163954767 chr6:163954753-163954764 chr6:163954754-163954764 chr6:163954754-163954764
8	CEBPB	chr6:163954487-163954861	Hela-S3	cervix:	n/a	chr6:163954769-163954786
9	NR3C1	chr6:163954487-163954863	A549	lung:	n/a	chr6:163954755-163954764
10	JUN	chr6:163954490-163954830	HUVEC	blood vessel:	n/a	chr6:163954754-163954764 chr6:163954754-163954764 chr6:163954756-163954767 chr6:163954754-163954764 chr6:163954754-163954764 chr6:163954645-163954658
11	STAT3	chr6:163954562-163954940	MCF10A-Er-Src	breast:	n/a	chr6:163954775-163954782
12	FOS	chr6:163954471-163954961	HUVEC	blood vessel:	n/a	chr6:163954754-163954764 chr6:163954754-163954764 chr6:163954756-163954767 chr6:163954753-163954764 chr6:163954754-163954764 chr6:163954754-163954764
13	MAFK	chr6:163954542-163954873	HepG2	liver:	n/a	chr6:163954744-163954755 chr6:163954748-163954763 chr6:163954753-163954762
14	TCF12	chr6:163954389-163955014	A549	lung:	n/a	n/a
15	GATA3	chr6:163954434-163955020	SK-N-SH	brain:	n/a	n/a
16	JUND	chr6:163954500-163954979	HCT-116	colon:	n/a	chr6:163954754-163954764 chr6:163954754-163954764 chr6:163954756-163954767 chr6:163954754-163954764 chr6:163954754-163954764
17	CEBPB	chr6:163954494-163954962	IMR90	lung:	n/a	chr6:163954769-163954786
18	RXRA	chr6:163954408-163954978	SK-N-SH	brain:	n/a	n/a
19	MAFK	chr6:163954498-163954917	IMR90	lung:	n/a	chr6:163954744-163954755 chr6:163954748-163954763 chr6:163954753-163954762
20	FOS	chr6:163954513-163954938	MCF10A-Er-Src	breast:	n/a	chr6:163954754-163954764 chr6:163954754-163954764 chr6:163954756-163954767 chr6:163954753-163954764 chr6:163954754-163954764 chr6:163954754-163954764
21	MYC	chr6:163954541-163954886	MCF10A-Er-Src	breast:	n/a	n/a
22	TCF12	chr6:163954344-163954998	SK-N-SH	brain:	n/a	n/a
23	CEBPB	chr6:163954379-163955017	A549	lung:	n/a	chr6:163954769-163954786
24	SP1	chr6:163954404-163954922	A549	lung:	n/a	n/a
25	FOSL2	chr6:163954433-163954965	SK-N-SH	brain:	n/a	chr6:163954754-163954764 chr6:163954754-163954764 chr6:163954756-163954767 chr6:163954754-163954764 chr6:163954754-163954764
26	KAP1	chr6:163954315-163954964	HEK293	kidney:	n/a	n/a
27	MAFF	chr6:163954528-163954891	HepG2	liver:	n/a	n/a
28	TCF12	chr6:163954448-163955117	SK-N-SH	brain:	n/a	n/a
29	MYC	chr6:163954553-163954953	MCF10A-Er-Src	breast:	n/a	n/a
30	FOS	chr6:163954477-163954947	MCF10A-Er-Src	breast:	n/a	chr6:163954754-163954764 chr6:163954754-163954764 chr6:163954756-163954767 chr6:163954753-163954764 chr6:163954754-163954764 chr6:163954754-163954764
31	NR3C1	chr6:163954533-163954839	A549	lung:	n/a	chr6:163954755-163954764
32	NR3C1	chr6:163954451-163954882	A549	lung:	n/a	chr6:163954755-163954764
33	NR3C1	chr6:163954428-163954835	A549	lung:	n/a	chr6:163954755-163954764
34	FOSL2	chr6:163954485-163954977	A549	lung:	n/a	chr6:163954754-163954764 chr6:163954754-163954764 chr6:163954756-163954767 chr6:163954754-163954764 chr6:163954754-163954764
35	NFIC	chr6:163954394-163954969	SK-N-SH	brain:	n/a	n/a
36	SP1	chr6:163954425-163954922	A549	lung:	n/a	n/a
37	RCOR1	chr6:163954315-163955227	IMR90	lung:	n/a	n/a
38	FOXA1	chr6:163954282-163954889	A549	lung:	n/a	n/a
39	CEBPB	chr6:163954522-163954812	A549	lung:	n/a	chr6:163954769-163954786
40	POLR2A	chr6:163954533-163954930	SK-N-SH	brain:	n/a	n/a
41	ARID3A	chr6:163954423-163954851	HepG2	liver:	n/a	n/a
42	FOS	chr6:163954463-163954947	MCF10A-Er-Src	breast:	n/a	chr6:163954754-163954764 chr6:163954754-163954764 chr6:163954756-163954767 chr6:163954753-163954764 chr6:163954754-163954764 chr6:163954754-163954764
43	CEBPB	chr6:163954544-163954953	HCT-116	colon:	n/a	chr6:163954769-163954786
44	JUN	chr6:163954564-163954788	K562	blood:	n/a	chr6:163954754-163954764 chr6:163954754-163954764 chr6:163954756-163954767 chr6:163954754-163954764 chr6:163954754-163954764 chr6:163954645-163954658
45	CEBPB	chr6:163954515-163954806	K562	blood:	n/a	chr6:163954769-163954786
46	USF1	chr6:163954465-163954857	A549	lung:	n/a	n/a
47	JUND	chr6:163954460-163954907	HepG2	liver:	n/a	chr6:163954754-163954764 chr6:163954754-163954764 chr6:163954756-163954767 chr6:163954754-163954764 chr6:163954754-163954764
48	IRF1	chr6:163954466-163954793	K562	blood:	n/a	n/a
49	CEBPB	chr6:163954494-163954850	HepG2	liver:	n/a	chr6:163954769-163954786
50	CREB1	chr6:163954490-163954866	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:163947828..163950335-chr6:163953664..163955368,2	K562	blood:
2	chr6:163952879..163955434-chr6:163961662..163963741,2	K562	blood:
3	chr6:163947867..163950430-chr6:163952220..163954736,3	K562	blood:
4	chr6:163832850..163838270-chr6:163950827..163956360,5	K562	blood:

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

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

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]
rs13199835	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13202282	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16895015	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs1737328	0.82[CHB][hapmap]
rs17591955	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2143358	0.81[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2294698	0.94[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294703	0.82[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2294706	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2294709	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35442073	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3756879	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs3763197	0.82[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap]
rs3857504	0.83[JPT][hapmap]
rs3904720	0.83[JPT][hapmap]
rs41268571	0.82[ASN][1000 genomes]
rs4263561	0.89[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap]
rs4709716	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4709717	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4709718	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4709720	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4709722	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6455897	0.82[CHB][hapmap]
rs6931903	0.82[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap]
rs6939218	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs715020	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]
rs724826	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7758706	0.82[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap]
rs7772756	0.94[JPT][hapmap]
rs9346960	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9364688	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9364689	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9364691	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9364692	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]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9347760	QKI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 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	chr6:163939800-163956200	Enhancers	Brain Anterior Caudate	brain
7	chr6:163940200-163983000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr6:163944200-163957400	Enhancers	Brain Substantia Nigra	brain
9	chr6:163945000-163957400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:163945800-163955800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr6:163946200-163955800	Enhancers	Liver	Liver
12	chr6:163948400-163958400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr6:163948600-163959000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:163948600-163964600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:163949000-163958000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr6:163949200-163955800	Enhancers	Brain Germinal Matrix	brain
17	chr6:163949400-163959200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:163949600-163975200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:163949600-163992000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:163949600-163995400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:163950800-163956200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:163951000-163978800	Weak transcription	Fetal Kidney	kidney
23	chr6:163951200-163954600	Enhancers	HepG2	liver
24	chr6:163951200-163956000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:163951200-163956000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:163951200-163956000	Enhancers	NHLF	lung
27	chr6:163951200-163993200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:163951400-163954600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr6:163951400-163956200	Enhancers	HSMM	muscle
30	chr6:163951600-163985800	Weak transcription	Hela-S3	cervix
31	chr6:163951800-163956200	Enhancers	NHDF-Ad	bronchial
32	chr6:163951800-163973400	Weak transcription	Fetal Stomach	stomach
33	chr6:163952000-163956000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:163952000-163956200	Enhancers	Muscle Satellite Cultured Cells	--
35	chr6:163952000-163958600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr6:163952200-163954800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr6:163952200-163955800	Enhancers	NH-A	brain
38	chr6:163952200-163957000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr6:163952400-163954800	Enhancers	Fetal Heart	heart
40	chr6:163952400-163956200	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr6:163952400-163984400	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr6:163952600-163956000	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr6:163952600-163958000	Weak transcription	Ovary	ovary
44	chr6:163952600-163958400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:163952600-163959200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:163952600-163959400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:163952600-163960200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:163952600-163960400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr6:163952600-163960800	Enhancers	Brain Cingulate Gyrus	brain
50	chr6:163952600-163961400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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