Variant report

Variant	rs4709717
Chromosome Location	chr6:163894664-163894665
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:163892454..163895409-chr6:163896616..163898931,2	K562	blood:
2	chr6:163893040..163896029-chr6:163899899..163902855,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PACRG-2	chr6:163894452-163895192	NONHSAT115963

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1047935	0.86[EUR][1000 genomes]
rs11962088	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs13199835	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13202282	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16895015	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1737328	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs17591955	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs2143358	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2294698	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2294703	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2294706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2294707	0.81[ASN][1000 genomes]
rs2294709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35442073	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3756879	0.82[CHB][hapmap]
rs3763197	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4263561	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs4709716	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	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4709720	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4709722	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6455897	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs6931903	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6939218	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs715020	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs724826	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73015387	0.82[ASN][1000 genomes]
rs7758706	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7772756	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs9346960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9347760	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]
rs9364688	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9364689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9364691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9364692	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]

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
rs4709717	QKI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163878800-163910200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:163880600-163896600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:163880600-163897600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:163880600-163903200	Weak transcription	Pancreas	Pancrea
5	chr6:163880600-163906600	Weak transcription	Gastric	stomach
6	chr6:163881800-163897600	Weak transcription	Ovary	ovary
7	chr6:163881800-163901000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:163881800-163910800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:163882000-163899800	Weak transcription	Placenta	Placenta
10	chr6:163882000-163900000	Weak transcription	Fetal Thymus	thymus
11	chr6:163882000-163906600	Weak transcription	Thymus	Thymus
12	chr6:163883000-163895800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:163883000-163900800	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr6:163883000-163900800	Weak transcription	NH-A	brain
15	chr6:163883000-163906800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr6:163883800-163897000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:163884000-163895800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:163887200-163900000	Weak transcription	Fetal Stomach	stomach
19	chr6:163888400-163902800	Weak transcription	Right Atrium	heart
20	chr6:163888400-163908200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:163889400-163897400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:163890000-163900200	Weak transcription	Liver	Liver
23	chr6:163890000-163906200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:163890800-163911400	Weak transcription	Osteobl	bone
25	chr6:163891000-163896000	Weak transcription	Brain Germinal Matrix	brain
26	chr6:163891400-163898600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:163891400-163900000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr6:163891400-163900000	Weak transcription	Lung	lung
29	chr6:163891400-163906400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:163891400-163910200	Weak transcription	HUVEC	blood vessel
31	chr6:163891600-163896400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:163891600-163900200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:163891600-163905000	Weak transcription	K562	blood
34	chr6:163891800-163895200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr6:163891800-163899400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr6:163891800-163902000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:163892000-163896200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:163892000-163904200	Weak transcription	NHDF-Ad	bronchial
39	chr6:163892200-163899200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:163892200-163899800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:163892200-163911400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr6:163892400-163897400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:163892400-163899800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr6:163892400-163899800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:163892400-163903400	Weak transcription	Primary B cells from cord blood	blood
46	chr6:163892600-163896400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:163892600-163896800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr6:163892600-163899400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:163892600-163906600	Weak transcription	NHEK	skin
50	chr6:163892600-163910400	Weak transcription	HMEC	breast

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