Variant report

Variant	rs942640
Chromosome Location	chr6:33686442-33686443
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33684071..33687779-chr6:33863332..33865982,3	MCF-7	breast:
2	chr6:33684529..33686540-chr6:33729478..33731636,2	MCF-7	breast:
3	chr6:33670443..33672859-chr6:33684999..33687830,2	K562	blood:
4	chr6:33680227..33683145-chr6:33684696..33687420,2	K562	blood:
5	chr6:33674250..33675922-chr6:33684521..33687700,3	K562	blood:
6	chr6:33676188..33679535-chr6:33684532..33687209,3	MCF-7	breast:
7	chr6:33684753..33687394-chr6:33728535..33731247,2	MCF-7	breast:
8	chr6:33680227..33683293-chr6:33684221..33688907,5	K562	blood:
9	chr6:33686168..33688632-chr6:33755438..33757308,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000161904	Chromatin interaction
ENSG00000137288	Chromatin interaction
ENSG00000249346	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1014933	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947430	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10947434	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10947435	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11759396	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1555965	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2147656	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2147657	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2229642	0.92[EUR][1000 genomes]
rs2274458	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281829	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2296736	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2296738	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2296739	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2296741	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2296742	0.92[EUR][1000 genomes]
rs28651968	0.81[AMR][1000 genomes]
rs2966	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3227	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3818521	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3818523	0.93[EUR][1000 genomes]
rs3818524	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3818525	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3818527	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3818529	0.93[EUR][1000 genomes]
rs3818530	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4711336	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4711337	0.92[EUR][1000 genomes]
rs4711338	0.92[EUR][1000 genomes]
rs4711339	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711340	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4711343	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4713655	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4713658	0.92[EUR][1000 genomes]
rs4713659	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713660	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713661	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713662	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713663	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4713665	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4713666	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713667	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713669	0.89[EUR][1000 genomes]
rs4713670	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4713671	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4713672	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4713674	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs509539	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs560111	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60704560	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6457739	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6904816	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6916949	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917140	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928010	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6938056	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs749338	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs749847	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs753890	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs754404	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs764752	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs764754	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7739505	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7759668	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7770465	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs791902	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs791903	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9348924	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9348925	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9366828	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9368773	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9368776	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9380375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394162	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9394163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942641	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs942643	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9469566	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs942640	ITPR3	cis	Whole Blood	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33680000-33689400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:33680000-33690000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:33680000-33690200	Weak transcription	Psoas Muscle	Psoas
4	chr6:33680000-33693000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:33680000-33695200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:33680000-33695800	Weak transcription	Spleen	Spleen
7	chr6:33680000-33696200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:33680000-33698400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:33680000-33705000	Weak transcription	Brain Angular Gyrus	brain
10	chr6:33681800-33689200	Enhancers	Pancreas	Pancrea
11	chr6:33683000-33686600	Enhancers	Stomach Mucosa	stomach
12	chr6:33684000-33686600	Enhancers	Left Ventricle	heart
13	chr6:33684000-33687000	Enhancers	HMEC	breast
14	chr6:33684200-33687400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:33684200-33688200	Enhancers	Fetal Lung	lung
16	chr6:33684400-33688000	Weak transcription	Gastric	stomach
17	chr6:33684600-33688200	Enhancers	Fetal Brain Male	brain
18	chr6:33684600-33688600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:33684800-33686600	Enhancers	Rectal Smooth Muscle	rectum
20	chr6:33685000-33686600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr6:33685000-33686600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:33685000-33686600	Enhancers	Fetal Stomach	stomach
23	chr6:33685000-33686600	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr6:33685000-33686800	Enhancers	Fetal Muscle Leg	muscle
25	chr6:33685000-33687400	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr6:33685200-33686600	Enhancers	Fetal Muscle Trunk	muscle
27	chr6:33685200-33688000	Weak transcription	GM12878-XiMat	blood
28	chr6:33685200-33693400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:33685600-33686600	Enhancers	Brain Germinal Matrix	brain
30	chr6:33685800-33686600	Enhancers	Right Atrium	heart
31	chr6:33685800-33687000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:33685800-33687000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:33686000-33686600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:33686000-33686600	Enhancers	Muscle Satellite Cultured Cells	--
35	chr6:33686000-33686600	Enhancers	Brain Anterior Caudate	brain
36	chr6:33686000-33686600	Enhancers	Fetal Brain Female	brain
37	chr6:33686000-33686600	Enhancers	Right Ventricle	heart
38	chr6:33686000-33686800	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr6:33686000-33686800	Enhancers	Lung	lung
40	chr6:33686000-33688000	Enhancers	Brain Substantia Nigra	brain
41	chr6:33686200-33686600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:33686200-33686600	Enhancers	Colonic Mucosa	Colon
43	chr6:33686200-33686600	Enhancers	HSMM	muscle
44	chr6:33686200-33686600	Flanking Active TSS	NHEK	skin
45	chr6:33686200-33686800	Enhancers	HSMMtube	muscle
46	chr6:33686200-33687400	Enhancers	Esophagus	oesophagus
47	chr6:33686200-33700200	Weak transcription	Liver	Liver
48	chr6:33686400-33686600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:33686400-33686600	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr6:33686400-33689600	Weak transcription	Brain Hippocampus Middle	brain

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