Variant report

Variant	rs2759396
Chromosome Location	chr6:163882444-163882445
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	chr6:163878253..163881131-chr6:163881459..163884552,3	K562	blood:
2	chr6:163881425..163884051-chr6:164006654..164009076,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12210561	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1230320	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234977	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572434	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1614869	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1737330	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1737331	1.00[CHB][hapmap]
rs1737610	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1744929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1764022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1764023	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2259476	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2259477	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2475390	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2475877	0.84[EUR][1000 genomes]
rs2757573	1.00[CHB][hapmap]
rs2757575	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2757576	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2757584	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902395	1.00[CHB][hapmap]
rs6939187	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73021476	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7744302	1.00[CHB][hapmap]
rs7754222	1.00[CHB][hapmap]
rs7764847	1.00[CHB][hapmap]
rs783137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs803612	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9347747	0.83[EUR][1000 genomes]
rs9347752	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9347765	1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9347766	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9365575	1.00[CHB][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9458843	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9458860	1.00[CHB][hapmap]

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
rs2759396	QKI	cis	Whole Blood	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

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	chr6:163879400-163884200	Weak transcription	HepG2	liver
5	chr6:163879400-163891000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:163880000-163882800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr6:163880200-163882800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:163880400-163886000	Enhancers	Fetal Heart	heart
9	chr6:163880400-163888800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:163880600-163882600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:163880600-163882800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:163880600-163883000	Active TSS	Right Atrium	heart
13	chr6:163880600-163883200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:163880600-163890800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:163880600-163891000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:163880600-163891000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:163880600-163896600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:163880600-163897600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:163880600-163903200	Weak transcription	Pancreas	Pancrea
20	chr6:163880600-163906600	Weak transcription	Gastric	stomach
21	chr6:163881000-163882600	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr6:163881200-163882800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:163881400-163882600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:163881400-163882600	Active TSS	NHDF-Ad	bronchial
25	chr6:163881600-163882600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr6:163881600-163890400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr6:163881800-163882600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:163881800-163882600	Active TSS	Brain Angular Gyrus	brain
29	chr6:163881800-163882600	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr6:163881800-163882600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:163881800-163882800	Weak transcription	Right Ventricle	heart
32	chr6:163881800-163883400	Enhancers	Brain Germinal Matrix	brain
33	chr6:163881800-163883800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:163881800-163886000	Weak transcription	Fetal Lung	lung
35	chr6:163881800-163886400	Enhancers	Brain Anterior Caudate	brain
36	chr6:163881800-163886400	Weak transcription	Fetal Stomach	stomach
37	chr6:163881800-163888000	Weak transcription	Left Ventricle	heart
38	chr6:163881800-163888200	Weak transcription	Aorta	Aorta
39	chr6:163881800-163889000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:163881800-163890200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr6:163881800-163890600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr6:163881800-163890600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:163881800-163897600	Weak transcription	Ovary	ovary
44	chr6:163881800-163901000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:163881800-163910800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr6:163882000-163882600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:163882000-163882600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr6:163882000-163882600	Weak transcription	HSMMtube	muscle
49	chr6:163882000-163882800	Enhancers	Colon Smooth Muscle	Colon
50	chr6:163882000-163882800	Enhancers	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links