Variant report

Variant	rs9840079
Chromosome Location	chr3:53892641-53892642
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53888852..53890407-chr3:53890829..53893730,2	K562	blood:
2	chr3:53878629..53881188-chr3:53889615..53893181,4	MCF-7	breast:
3	chr3:53889294..53893230-chr3:53913823..53917660,4	K562	blood:
4	chr3:53891718..53893662-chr3:53914983..53917466,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000056736	Chromatin interaction
ENSG00000016391	Chromatin interaction
ENSG00000113812	Chromatin interaction
ENSG00000222888	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10440151	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1046677	1.00[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1134092	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1157175	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13072145	0.97[ASN][1000 genomes]
rs13315972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982172	0.82[EUR][1000 genomes]
rs1992155	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2083127	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276846	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3733073	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3733081	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3816144	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821867	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4569647	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687757	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687763	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7624599	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7636856	0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs893367	1.00[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9311516	0.97[ASN][1000 genomes]
rs9311518	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9822471	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840362	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9869505	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9878207	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9878562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs999514	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs9840079	IL17RB	cis	cerebellum	SCAN
rs9840079	ACTR8	cis	lymphoblastoid	seeQTL
rs9840079	RP11-884K10.7	cis	Muscle Skeletal	GTEx
rs9840079	ACTR8	cis	parietal	SCAN
rs9840079	IL17RB	cis	parietal	SCAN
rs9840079	ACTR8	cis	cerebellum	SCAN
rs9840079	SFMBT1	cis	cerebellum	SCAN
rs9840079	IL17RB	cis	Whole Blood	GTEx
rs9840079	SELK	Cis_1M	lymphoblastoid	RTeQTL
rs9840079	SPATA12	cis	cerebellum	SCAN
rs9840079	CHDH	cis	cerebellum	SCAN
rs9840079	IL17RB	cis	Cerebellum	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53881000-53893200	Weak transcription	Ovary	ovary
2	chr3:53881200-53895000	Weak transcription	A549	lung
3	chr3:53881200-53895800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:53881400-53892800	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:53881400-53893000	Weak transcription	Brain Angular Gyrus	brain
6	chr3:53881400-53893000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:53884000-53895800	Strong transcription	HepG2	liver
8	chr3:53884400-53892800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:53885000-53901000	Weak transcription	Fetal Heart	heart
10	chr3:53885400-53892800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:53885400-53895200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:53885600-53896600	Weak transcription	Right Ventricle	heart
13	chr3:53886200-53897200	Weak transcription	Colonic Mucosa	Colon
14	chr3:53887800-53892800	Weak transcription	Lung	lung
15	chr3:53887800-53898400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:53888400-53914600	Weak transcription	Stomach Mucosa	stomach
17	chr3:53888800-53894400	Weak transcription	Primary T cells from cord blood	blood
18	chr3:53889000-53901400	Weak transcription	Esophagus	oesophagus
19	chr3:53889200-53892800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:53889200-53894400	Strong transcription	Fetal Intestine Small	intestine
21	chr3:53889400-53892800	Enhancers	GM12878-XiMat	blood
22	chr3:53889600-53892800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:53889600-53892800	Weak transcription	Thymus	Thymus
24	chr3:53889600-53895200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:53889600-53896000	Strong transcription	Pancreas	Pancrea
26	chr3:53889600-53913800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:53889800-53892800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:53889800-53892800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:53889800-53893200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:53889800-53895400	Weak transcription	NHDF-Ad	bronchial
31	chr3:53890000-53892800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr3:53890000-53895800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:53890000-53904000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:53890200-53892800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:53890200-53894400	Weak transcription	Aorta	Aorta
36	chr3:53890200-53895800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:53890400-53894400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:53890400-53895200	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:53890400-53898600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:53890400-53898800	Weak transcription	NH-A	brain
41	chr3:53890400-53903600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr3:53890600-53893000	Weak transcription	HSMM	muscle
43	chr3:53890800-53893000	Weak transcription	Placenta	Placenta
44	chr3:53890800-53893200	Weak transcription	HSMMtube	muscle
45	chr3:53890800-53893400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:53890800-53914600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:53891000-53892800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:53891000-53895000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:53891000-53895800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:53891000-53898000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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