Variant report

Variant	rs12043409
Chromosome Location	chr1:85678459-85678460
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85665001..85668975-chr1:85676628..85680834,4	K562	blood:
2	chr1:85671412..85673283-chr1:85677641..85680596,2	K562	blood:
3	chr1:85665751..85667554-chr1:85677645..85679549,2	MCF-7	breast:
4	chr1:85664392..85672702-chr1:85677833..85684054,17	MCF-7	breast:
5	chr1:85666226..85668232-chr1:85676628..85679487,2	K562	blood:

Variant related genes	Relation type
ENSG00000097096	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11805650	0.95[EUR][1000 genomes]
rs12021868	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12022814	0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12023751	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12028707	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12034359	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12034501	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12034937	0.95[EUR][1000 genomes]
rs12036276	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12039804	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12040408	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12041155	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12045141	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1674179	1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs17099217	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes]
rs17121656	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes]
rs17121745	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes]
rs17121935	1.00[AFR][1000 genomes]
rs17121978	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2305930	1.00[AFR][1000 genomes]
rs2305931	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[AFR][1000 genomes]
rs28410552	1.00[AFR][1000 genomes]
rs3013111	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs41289039	1.00[AFR][1000 genomes]
rs56191061	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs57222060	1.00[AFR][1000 genomes]
rs57516443	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs58068482	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs58246117	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs58604582	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs58659750	1.00[AFR][1000 genomes]
rs59030463	1.00[AFR][1000 genomes]
rs59248240	1.00[AFR][1000 genomes]
rs60866399	1.00[AFR][1000 genomes]
rs72482805	0.95[EUR][1000 genomes]
rs7513769	0.95[EUR][1000 genomes]
rs817387	0.93[EUR][1000 genomes]
rs817395	0.93[EUR][1000 genomes]
rs817413	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs817414	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs817418	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs817427	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs817429	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs817430	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs817431	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs817432	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs817435	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs817437	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs817439	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs817440	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs817452	0.89[CHB][hapmap];0.86[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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85668000-85689000	Weak transcription	Gastric	stomach
2	chr1:85668600-85680800	Weak transcription	K562	blood
3	chr1:85670800-85679400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:85673200-85681200	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:85673800-85690400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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