Variant report

Variant	rs11079799
Chromosome Location	chr17:45956073-45956074
allele	A/G
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	chr17:45954517..45959288-chr17:45971279..45974982,5	MCF-7	breast:
2	chr17:45955326..45957422-chr17:46018583..46020221,2	MCF-7	breast:
3	chr17:45955663..45958108-chr17:45961130..45962855,2	K562	blood:
4	chr17:45927022..45929446-chr17:45953894..45957951,3	K562	blood:
5	chr17:45955819..45958170-chr17:45960377..45962855,3	K562	blood:
6	chr17:45949402..45954335-chr17:45955513..45959303,4	K562	blood:
7	chr17:45954484..45959209-chr17:45960047..45963266,6	MCF-7	breast:
8	chr17:45927880..45930031-chr17:45955168..45956682,2	MCF-7	breast:
9	chr17:45954562..45956149-chr17:45971370..45973332,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000234494	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000108439	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10428	0.82[JPT][hapmap]
rs11079797	0.82[GIH][hapmap];0.82[JPT][hapmap]
rs11649750	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11871969	1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs16948662	0.82[JPT][hapmap]
rs17617010	0.82[JPT][hapmap]
rs2010952	0.82[JPT][hapmap]
rs2074185	0.93[GIH][hapmap];1.00[JPT][hapmap]
rs2325714	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4793688	0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4794224	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4794318	0.82[JPT][hapmap]
rs60123006	0.82[EUR][1000 genomes]
rs6503875	0.82[JPT][hapmap]
rs6503897	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7212099	0.82[JPT][hapmap]
rs7214694	0.82[JPT][hapmap]
rs916798	0.82[JPT][hapmap]
rs9904503	0.82[JPT][hapmap]

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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908573	chr17:45858487-45956073	Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11079799	ACBD4	cis	cerebellum	SCAN
rs11079799	KRTAP4-1	cis	parietal	SCAN
rs11079799	CNTNAP1	cis	cerebellum	SCAN
rs11079799	AOC3	cis	parietal	SCAN
rs11079799	SCRN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45953600-45956200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr17:45954400-45957200	Enhancers	Placenta	Placenta
3	chr17:45954600-45956200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr17:45954600-45956200	Enhancers	Lung	lung
5	chr17:45954600-45956800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr17:45954600-45956800	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr17:45954600-45957000	Enhancers	Primary hematopoietic stem cells	blood
8	chr17:45954600-45957400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
9	chr17:45954600-45964400	Enhancers	Fetal Intestine Large	intestine
10	chr17:45954800-45956400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr17:45954800-45956400	Enhancers	Fetal Lung	lung
12	chr17:45954800-45956600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr17:45954800-45956600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr17:45954800-45956800	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr17:45954800-45956800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr17:45954800-45956800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr17:45955000-45956200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr17:45955000-45956400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
19	chr17:45955200-45956400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr17:45955200-45956400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr17:45955200-45956600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr17:45955200-45956800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr17:45955200-45956800	Enhancers	HSMMtube	muscle
24	chr17:45955200-45957000	Enhancers	HSMM	muscle
25	chr17:45955400-45956600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr17:45955400-45956600	Enhancers	Fetal Intestine Small	intestine
27	chr17:45955400-45956600	Enhancers	Placenta Amnion	Placenta Amnion
28	chr17:45955400-45956800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr17:45955400-45956800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr17:45955400-45956800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr17:45955400-45956800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr17:45955400-45956800	Enhancers	NH-A	brain
33	chr17:45955600-45956200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr17:45955600-45956200	Bivalent Enhancer	Fetal Thymus	thymus
35	chr17:45955600-45956400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr17:45955600-45956400	Enhancers	A549	lung
37	chr17:45955600-45956800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr17:45955600-45956800	Enhancers	NHDF-Ad	bronchial
39	chr17:45955800-45956200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
40	chr17:45955800-45956400	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr17:45955800-45956400	Bivalent Enhancer	HepG2	liver
42	chr17:45955800-45956800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr17:45955800-45956800	Enhancers	HMEC	breast
44	chr17:45955800-45956800	Flanking Active TSS	Osteobl	bone
45	chr17:45955800-45959400	Weak transcription	Fetal Kidney	kidney
46	chr17:45956000-45956400	Enhancers	Muscle Satellite Cultured Cells	--
47	chr17:45956000-45956800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr17:45956000-45957000	Enhancers	K562	blood

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