Variant report

Variant	rs6542245
Chromosome Location	chr2:111749531-111749532
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr2:111749329-111750150	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:111741788..111745598-chr2:111748398..111751516,4	MCF-7	breast:

Variant related genes	Relation type
ACOXL	TF binding region
ENSG00000153093	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10167918	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs10181859	0.82[EUR][1000 genomes]
rs10191949	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs10197016	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs1038371	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs1157454	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs11894723	0.82[EUR][1000 genomes]
rs12105855	0.91[CEU][hapmap]
rs12993549	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs1471692	0.91[CEU][hapmap]
rs1483534	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs1483536	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs17482961	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17548346	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4848366	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs4849314	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4849316	0.83[CEU][hapmap]
rs4849325	0.81[EUR][1000 genomes]
rs4849331	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs62161501	0.82[EUR][1000 genomes]
rs62161543	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6542250	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs6737041	0.82[EUR][1000 genomes]
rs7581900	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7589645	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs7599682	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs958347	0.91[CEU][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874839	chr2:111400934-111868010	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv997829	chr2:111486961-111780537	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv834330	chr2:111593290-111789447	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1004949	chr2:111607532-111780719	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1002568	chr2:111607532-111781442	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1005665	chr2:111610107-111762039	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv535892	chr2:111610107-111762039	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111738600-111751800	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr2:111743400-111751800	Weak transcription	Fetal Intestine Small	intestine
3	chr2:111746200-111754200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:111746800-111752000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:111747600-111750000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:111749200-111750400	Enhancers	Fetal Stomach	stomach
7	chr2:111749200-111752600	Enhancers	Fetal Lung	lung
8	chr2:111749200-111756200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr2:111749400-111749800	Active TSS	Stomach Smooth Muscle	stomach
10	chr2:111749400-111750000	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr2:111749400-111750200	Enhancers	Colon Smooth Muscle	Colon
12	chr2:111749400-111750400	Enhancers	Fetal Muscle Leg	muscle

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