Variant report

Variant	rs12955201
Chromosome Location	chr18:43643435-43643436
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:43642172..43644592-chr18:43648279..43650859,2	MCF-7	breast:
2	chr18:43641479..43644976-chr18:43650874..43653510,3	K562	blood:

Variant related genes	Relation type
ENSG00000152229	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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]
rs12959752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12961167	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12963615	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7240076	1.00[JPT][hapmap]
rs7244921	0.89[GIH][hapmap]
rs7359798	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]
rs7359800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12955201	ATP5A1	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

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	chr18:43633800-43647600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr18:43636200-43644000	Weak transcription	Osteobl	bone
7	chr18:43636400-43644400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr18:43636400-43647000	Weak transcription	Liver	Liver
9	chr18:43636400-43649200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr18:43636400-43650200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr18:43636600-43649600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr18:43637000-43650000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr18:43640400-43644200	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr18:43640800-43650400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr18:43641000-43648800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr18:43641000-43650000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr18:43641000-43650800	Weak transcription	Fetal Intestine Small	intestine
18	chr18:43641400-43644000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr18:43641400-43644800	Enhancers	HMEC	breast
20	chr18:43641400-43648800	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr18:43641600-43644400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr18:43641600-43649000	Weak transcription	Left Ventricle	heart
23	chr18:43641800-43644000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr18:43641800-43645000	Enhancers	NHEK	skin
25	chr18:43642000-43644800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr18:43642000-43645000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr18:43642200-43643800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr18:43642200-43644800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr18:43642200-43646200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr18:43642200-43646200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr18:43642200-43651000	Weak transcription	Gastric	stomach
32	chr18:43642400-43643600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr18:43642400-43643800	Weak transcription	GM12878-XiMat	blood
34	chr18:43642400-43644400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr18:43642400-43651200	Weak transcription	Lung	lung
36	chr18:43643000-43643600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr18:43643200-43644800	Enhancers	K562	blood
38	chr18:43643200-43646400	Weak transcription	Spleen	Spleen
39	chr18:43643400-43644400	Weak transcription	Placenta	Placenta
40	chr18:43643400-43645000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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