Variant report

Variant	rs7359798
Chromosome Location	chr18:43648999-43649000
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:43642172..43644592-chr18:43648279..43650859,2	MCF-7	breast:
2	chr18:43640422..43642180-chr18:43647918..43649817,3	K562	blood:
3	chr18:43647683..43650654-chr18:43651658..43653260,2	K562	blood:

Variant related genes	Relation type
ENSG00000152229	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11082509	0.89[GIH][hapmap]
rs11659478	0.83[ASN][1000 genomes]
rs11664314	1.00[JPT][hapmap]
rs11664743	1.00[JPT][hapmap]
rs11874712	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12954944	0.84[GIH][hapmap]
rs12955201	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12959752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12961167	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12963615	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13381709	0.89[GIH][hapmap]
rs1800636	0.89[GIH][hapmap]
rs1800639	0.89[GIH][hapmap]
rs1800640	0.89[GIH][hapmap]
rs2298787	0.89[GIH][hapmap]
rs34003734	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7240076	1.00[JPT][hapmap]
rs7244921	0.89[GIH][hapmap]
rs7359800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8085444	0.96[ASN][1000 genomes]
rs8088881	0.89[GIH][hapmap]
rs8089150	0.89[GIH][hapmap]
rs8089153	1.00[JPT][hapmap]
rs8092674	0.89[GIH][hapmap]
rs8095374	1.00[JPT][hapmap]
rs8095608	0.89[GIH][hapmap]
rs9783888	0.92[ASN][1000 genomes]
rs9807399	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944637	0.96[ASN][1000 genomes]
rs9947908	0.96[ASN][1000 genomes]
rs9955853	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064882	chr18:43558343-43687674	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543693	chr18:43558343-43687674	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1062024	chr18:43589516-43749410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv543694	chr18:43589516-43749410	Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7359798	ATP5A1	cis	parietal	SCAN
rs7359798	ATP5A1	cis	multi-tissue	Pritchard

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43608600-43651000	Weak transcription	Esophagus	oesophagus
2	chr18:43632400-43651200	Weak transcription	Pancreas	Pancrea
3	chr18:43633200-43651200	Weak transcription	HSMMtube	muscle
4	chr18:43633400-43650200	Weak transcription	NHLF	lung
5	chr18:43636400-43649200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr18:43636400-43650200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr18:43636600-43649600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr18:43637000-43650000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr18:43640800-43650400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr18:43641000-43650000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr18:43641000-43650800	Weak transcription	Fetal Intestine Small	intestine
12	chr18:43641600-43649000	Weak transcription	Left Ventricle	heart
13	chr18:43642200-43651000	Weak transcription	Gastric	stomach
14	chr18:43642400-43651200	Weak transcription	Lung	lung
15	chr18:43644200-43649400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr18:43644800-43650000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr18:43645000-43649000	Weak transcription	Placenta	Placenta
18	chr18:43645000-43650000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr18:43645200-43650800	Weak transcription	Osteobl	bone
20	chr18:43646200-43650800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr18:43646800-43650800	Weak transcription	Spleen	Spleen
22	chr18:43647000-43649000	Weak transcription	Fetal Intestine Large	intestine
23	chr18:43647600-43649000	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr18:43647600-43651000	Weak transcription	Primary T cells from cord blood	blood
25	chr18:43647800-43650800	Weak transcription	Colon Smooth Muscle	Colon
26	chr18:43648000-43650800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr18:43648000-43651600	Weak transcription	Hela-S3	cervix
28	chr18:43648400-43651000	Enhancers	Liver	Liver
29	chr18:43648600-43649000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr18:43648600-43649000	Enhancers	HMEC	breast
31	chr18:43648600-43649000	Enhancers	NHEK	skin
32	chr18:43648600-43649200	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr18:43648600-43649200	Enhancers	Adipose Nuclei	Adipose
34	chr18:43648600-43649800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr18:43648600-43651000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr18:43648800-43649000	Enhancers	Primary B cells from cord blood	blood
37	chr18:43648800-43649000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr18:43648800-43649000	Enhancers	Brain Substantia Nigra	brain
39	chr18:43648800-43649200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr18:43648800-43649200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
41	chr18:43648800-43649200	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr18:43648800-43649200	Enhancers	NH-A	brain
43	chr18:43648800-43649400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr18:43648800-43649400	Enhancers	K562	blood
45	chr18:43648800-43649800	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr18:43648800-43650200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr18:43648800-43650200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr18:43648800-43650400	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr18:43648800-43650600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr18:43648800-43650800	Enhancers	Primary T cells fromperipheralblood	blood

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