Variant report

Variant	rs9346960
Chromosome Location	chr6:163885290-163885291
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:163879929..163881986-chr6:163883834..163886314,2	K562	blood:
2	chr6:163882705..163885341-chr6:163888682..163891213,3	K562	blood:
3	chr6:163878553..163880705-chr6:163884842..163887651,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs1047935	0.84[EUR][1000 genomes]
rs11962088	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs13199835	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13202282	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16895015	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1737328	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs17591955	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs2143358	0.83[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2294698	1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap]
rs2294703	0.89[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2294706	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2294709	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35442073	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3756879	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs3763197	0.89[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs4263561	0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs4709716	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]
rs4709717	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]
rs4709718	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4709720	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4709722	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6455897	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs6931903	0.89[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs6939218	0.83[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs715020	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]
rs724826	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73015387	0.85[ASN][1000 genomes]
rs7758706	0.89[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7772756	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs9347760	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	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9364689	0.84[ASW][hapmap];1.00[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];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[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];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9364692	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]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9346960	QKI	Cis_1M	lymphoblastoid	RTeQTL
rs9346960	LOC285796	cis	lymphoblastoid	seeQTL
rs9346960	SESTD1	trans	cerebellum	SCAN

Chromatin state (count:92 , 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	chr6:163879200-163891000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:163879200-163891200	Weak transcription	Fetal Kidney	kidney
4	chr6:163879400-163891000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:163880400-163886000	Enhancers	Fetal Heart	heart
6	chr6:163880400-163888800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:163880600-163890800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:163880600-163891000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:163880600-163891000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:163880600-163896600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:163880600-163897600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:163880600-163903200	Weak transcription	Pancreas	Pancrea
13	chr6:163880600-163906600	Weak transcription	Gastric	stomach
14	chr6:163881600-163890400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:163881800-163886000	Weak transcription	Fetal Lung	lung
16	chr6:163881800-163886400	Enhancers	Brain Anterior Caudate	brain
17	chr6:163881800-163886400	Weak transcription	Fetal Stomach	stomach
18	chr6:163881800-163888000	Weak transcription	Left Ventricle	heart
19	chr6:163881800-163888200	Weak transcription	Aorta	Aorta
20	chr6:163881800-163889000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:163881800-163890200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:163881800-163890600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:163881800-163890600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:163881800-163897600	Weak transcription	Ovary	ovary
25	chr6:163881800-163901000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:163881800-163910800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:163882000-163885600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr6:163882000-163885800	Weak transcription	Fetal Muscle Leg	muscle
29	chr6:163882000-163886600	Weak transcription	NHEK	skin
30	chr6:163882000-163887200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:163882000-163890600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr6:163882000-163891000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr6:163882000-163899800	Weak transcription	Placenta	Placenta
34	chr6:163882000-163900000	Weak transcription	Fetal Thymus	thymus
35	chr6:163882000-163906600	Weak transcription	Thymus	Thymus
36	chr6:163882200-163888200	Enhancers	Brain Cingulate Gyrus	brain
37	chr6:163882200-163890600	Weak transcription	A549	lung
38	chr6:163882200-163890600	Weak transcription	Osteobl	bone
39	chr6:163882600-163888000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:163882800-163886400	Strong transcription	K562	blood
41	chr6:163882800-163887600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr6:163882800-163887800	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:163882800-163888200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:163882800-163890400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:163882800-163890800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:163883000-163886000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr6:163883000-163886400	Weak transcription	Primary B cells from cord blood	blood
48	chr6:163883000-163887600	Weak transcription	HSMM	muscle
49	chr6:163883000-163887800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:163883000-163887800	Weak transcription	NHLF	lung

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