Variant report

Variant	rs1228020
Chromosome Location	chr11:47953477-47953478
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47868025..47869927-chr11:47953160..47956003,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000030066	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10769307	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10838790	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039473	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11039480	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12099166	1.00[JPT][hapmap]
rs12270546	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12272781	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12273589	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1227997	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1227999	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1228000	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1228002	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1228004	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1228008	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1228018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1228019	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1228021	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1228022	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1228023	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12290628	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12294218	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12295364	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1681604	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1681627	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1681631	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1681637	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1729281	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1729294	0.93[EUR][1000 genomes]
rs1729297	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17727140	0.83[CEU][hapmap]
rs2626567	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697810	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2930188	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930189	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930192	0.84[EUR][1000 genomes]
rs2930195	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2950888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4752883	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4752886	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6485797	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7104376	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7111419	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7113640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7116080	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7117644	0.85[EUR][1000 genomes]
rs7119280	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73462871	0.88[ASN][1000 genomes]
rs73462874	0.88[ASN][1000 genomes]
rs73462875	0.88[ASN][1000 genomes]
rs7928153	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7932759	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7941441	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs900699	1.00[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv897326	chr11:47891334-48035474	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1228020	MTCH2	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47950400-47955600	Weak transcription	Thymus	Thymus
2	chr11:47950400-47963600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr11:47950600-47953800	Weak transcription	GM12878-XiMat	blood
4	chr11:47950600-47958800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr11:47950600-47959600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr11:47950800-47956000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr11:47950800-47959400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr11:47950800-47971800	Weak transcription	Fetal Thymus	thymus
9	chr11:47951000-47954200	Weak transcription	Primary B cells from cord blood	blood
10	chr11:47951000-47955000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr11:47951000-47958800	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr11:47952600-47954400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:47952600-47958400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr11:47952600-47959000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr11:47952800-47953600	Active TSS	A549	lung
16	chr11:47953000-47954000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:47953200-47953600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:47953200-47953600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr11:47953200-47954000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:47953200-47954200	Enhancers	Osteobl	bone
21	chr11:47953200-47954400	Enhancers	Muscle Satellite Cultured Cells	--
22	chr11:47953200-47958400	Weak transcription	Placenta	Placenta
23	chr11:47953400-47954000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr11:47953400-47954400	Enhancers	Hela-S3	cervix
25	chr11:47953400-47958400	Weak transcription	NHDF-Ad	bronchial
26	chr11:47953400-47959000	Weak transcription	NHLF	lung
27	chr11:47953400-47959600	Weak transcription	NH-A	brain

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