Variant report

Variant	rs12199545
Chromosome Location	chr6:11388943-11388944
allele	A/T
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:11388708..11391347-chr6:11433045..11435258,2	MCF-7	breast:
2	chr6:11252403..11254057-chr6:11387199..11390299,3	MCF-7	breast:
3	chr6:11356402..11359256-chr6:11386897..11390575,4	MCF-7	breast:
4	chr6:11222489..11224264-chr6:11387362..11389387,2	MCF-7	breast:
5	chr6:11343010..11348187-chr6:11388549..11393263,7	MCF-7	breast:
6	chr6:11229965..11235177-chr6:11385041..11393111,14	MCF-7	breast:
7	chr6:11230510..11233804-chr6:11387057..11390361,4	MCF-7	breast:
8	chr6:11387321..11394874-chr6:11409302..11416244,8	MCF-7	breast:
9	chr6:11342539..11346028-chr6:11385686..11392115,8	MCF-7	breast:
10	chr6:11172296..11174854-chr6:11388458..11391129,2	MCF-7	breast:
11	chr6:11388874..11392122-chr6:11413409..11415866,5	MCF-7	breast:
12	chr6:11384266..11387041-chr6:11387793..11390164,2	MCF-7	breast:
13	chr6:11288344..11289961-chr6:11388125..11390631,2	MCF-7	breast:
14	chr6:11386757..11389915-chr6:11410069..11412647,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000111859	Chromatin interaction
ENSG00000247925	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1012502	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1013678	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947204	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12193099	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12204242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208626	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12210644	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12215372	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12215715	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215894	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13198555	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13217274	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1810451	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3798752	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs4276494	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4533978	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4632886	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4711271	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4711272	0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5019594	0.87[CHB][hapmap]
rs6916534	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6918440	0.87[CHB][hapmap]
rs6932496	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7738560	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7768351	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9296000	0.86[CHB][hapmap]
rs9348868	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9357127	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9368701	0.82[ASN][1000 genomes]
rs9461714	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9469034	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]

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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv432848	chr6:11371614-11560114	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11382600-11389400	Weak transcription	Lung	lung
2	chr6:11382600-11392400	Weak transcription	Right Atrium	heart
3	chr6:11383200-11390200	Weak transcription	Spleen	Spleen
4	chr6:11383400-11392600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:11383600-11393000	Weak transcription	Small Intestine	intestine
6	chr6:11383800-11392600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:11385200-11389200	Enhancers	Primary B cells from cord blood	blood
8	chr6:11385200-11389800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:11385600-11390400	Enhancers	Primary B cells from peripheral blood	blood
10	chr6:11385800-11393400	Weak transcription	Aorta	Aorta
11	chr6:11386000-11393600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:11386600-11389400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr6:11386600-11389400	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr6:11386600-11392200	Enhancers	HepG2	liver
15	chr6:11386800-11389600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr6:11387200-11392800	Weak transcription	Stomach Mucosa	stomach
17	chr6:11387400-11389400	Weak transcription	HUVEC	blood vessel
18	chr6:11387400-11390200	Weak transcription	Fetal Lung	lung
19	chr6:11387400-11392400	Weak transcription	Fetal Intestine Small	intestine
20	chr6:11388000-11389200	ZNF genes & repeats	GM12878-XiMat	blood
21	chr6:11388000-11389600	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr6:11388400-11392200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr6:11388800-11389200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr6:11388800-11390800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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