Variant report

Variant	rs4709716
Chromosome Location	chr6:163875549-163875550
allele	C/G
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	SETDB1	chr6:163875518-163875994	U2OS	brain:	n/a	n/a
2	POLR2A	chr6:163874998-163875938	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:163860977..163864792-chr6:163871306..163876031,5	K562	blood:
2	chr6:163862457..163864512-chr6:163873673..163876031,2	K562	blood:

Variant related genes	Relation type
QKI	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1047935	0.84[EUR][1000 genomes]
rs11962088	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs13199835	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13202282	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16895015	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1737328	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs17591955	0.89[CHB][hapmap];0.91[JPT][hapmap]
rs1764011	0.82[JPT][hapmap]
rs2143358	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2294698	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2294703	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2294706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2294709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2475396	0.83[ASN][1000 genomes]
rs35442073	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3756879	0.84[CHB][hapmap]
rs3763197	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3857503	0.84[ASN][1000 genomes]
rs4263561	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs4709717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4709718	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4709720	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4709722	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6455897	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs6921172	0.80[ASN][1000 genomes]
rs6931903	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6939218	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs715020	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs724826	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73015309	0.84[ASN][1000 genomes]
rs73015318	0.84[ASN][1000 genomes]
rs73015387	0.82[ASN][1000 genomes]
rs7758706	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7771996	1.00[YRI][hapmap]
rs7772756	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9346960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9347760	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9364687	0.84[ASN][1000 genomes]
rs9364688	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9364689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9364691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9364692	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1797109	chr6:163834147-163908115	Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv523664	chr6:163858237-163907885	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4709716	QKI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163840800-163881400	Weak transcription	Fetal Stomach	stomach
2	chr6:163845400-163877800	Weak transcription	Fetal Muscle Leg	muscle
3	chr6:163848800-163878400	Weak transcription	Pancreas	Pancrea
4	chr6:163852000-163880000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:163852200-163875600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:163852200-163875600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:163858400-163876600	Weak transcription	Primary B cells from cord blood	blood
8	chr6:163859600-163876600	Weak transcription	HUVEC	blood vessel
9	chr6:163859600-163878000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:163860200-163876200	Weak transcription	HSMM	muscle
11	chr6:163860200-163876200	Weak transcription	NHLF	lung
12	chr6:163860200-163877800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:163860400-163876600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr6:163860800-163878400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:163860800-163880000	Weak transcription	Lung	lung
16	chr6:163862600-163878000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:163862800-163876400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr6:163862800-163878600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:163863000-163876800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr6:163863000-163880200	Weak transcription	Esophagus	oesophagus
21	chr6:163863200-163876400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr6:163863200-163879200	Weak transcription	Fetal Brain Male	brain
23	chr6:163863600-163876600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:163863600-163878400	Weak transcription	Primary T cells from cord blood	blood
25	chr6:163863600-163878800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:163863800-163877800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr6:163863800-163877800	Weak transcription	Placenta	Placenta
28	chr6:163863800-163878000	Weak transcription	HMEC	breast
29	chr6:163863800-163878200	Weak transcription	NHEK	skin
30	chr6:163863800-163878800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr6:163864600-163875600	Weak transcription	Right Atrium	heart
32	chr6:163864800-163876400	Enhancers	Brain Substantia Nigra	brain
33	chr6:163865000-163877000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:163865200-163881400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:163865400-163875600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr6:163865400-163875600	Weak transcription	Fetal Brain Female	brain
37	chr6:163865400-163877800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:163865400-163877800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:163865400-163878600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr6:163865400-163878800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr6:163865600-163876600	Weak transcription	K562	blood
42	chr6:163865600-163878000	Weak transcription	Fetal Kidney	kidney
43	chr6:163867000-163877000	Weak transcription	Psoas Muscle	Psoas
44	chr6:163867800-163876600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr6:163868000-163876400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr6:163868000-163876600	Weak transcription	Right Ventricle	heart
47	chr6:163868200-163876400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr6:163868800-163876200	Weak transcription	NHDF-Ad	bronchial
49	chr6:163869400-163876600	Weak transcription	HepG2	liver
50	chr6:163869400-163877600	Weak transcription	Muscle Satellite Cultured Cells	--

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