Variant report

Variant	rs644549
Chromosome Location	chr11:56615290-56615291
allele	A/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	EP300	chr11:56615262-56617108	SK-N-SH	brain:	n/a	chr11:56615941-56615954
2	EP300	chr11:56615147-56616484	A549	lung:	n/a	chr11:56615941-56615954
3	TCF12	chr11:56614909-56617181	A549	lung:	n/a	n/a
4	GATA3	chr11:56615063-56616287	A549	lung:	n/a	n/a
5	FOSL2	chr11:56615006-56617214	A549	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000255433	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1792515	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs479697	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs506223	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs509244	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs513618	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs514165	0.85[CEU][hapmap]
rs522662	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs540638	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs554574	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs556870	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs561116	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs564653	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs564841	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs596396	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs597733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61889068	0.86[AFR][1000 genomes]
rs624598	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs626464	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6591386	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7117250	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7939427	0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048328	chr11:56471984-56649908	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	esv2830406	chr11:56481955-56650124	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv468577	chr11:56503728-56704042	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv555101	chr11:56503728-56704042	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
5	nsv469960	chr11:56605222-56704042	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr11:56613200-56618400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr11:56613600-56617800	Enhancers	HMEC	breast
3	chr11:56614400-56621400	Weak transcription	Stomach Mucosa	stomach
4	chr11:56614600-56616800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr11:56614600-56617000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:56614800-56616400	Weak transcription	NHEK	skin
7	chr11:56615000-56615400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:56615000-56616800	Flanking Active TSS	A549	lung
9	chr11:56615200-56615400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr11:56615200-56615800	Enhancers	Fetal Muscle Leg	muscle
11	chr11:56615200-56616200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:56615200-56616400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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