Variant report

Variant	rs6888490
Chromosome Location	chr5:61440693-61440694
allele	A/G
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	POLR2A	chr5:61440651-61440704	MCF-7	breast:	n/a	n/a
2	CTCF	chr5:61440667-61440710	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
RN7SKP157	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11748847	0.85[AFR][1000 genomes]
rs1363783	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs3846461	1.00[AFR][1000 genomes]
rs4320208	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs737053	0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats 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 target site	36 gene(s)	inside rSNPs	diseases
2	nsv830317	chr5:61298840-61478113	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2757996	chr5:61403138-61687817	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv2759345	chr5:61403138-61748912	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv830318	chr5:61415713-61623320	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1022497	chr5:61424594-61470438	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1026425	chr5:61424594-61471448	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1025920	chr5:61424594-61471782	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2763457	chr5:61424606-61472050	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1017594	chr5:61425095-61471448	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv598322	chr5:61428137-61452417	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv462201	chr5:61428137-61461609	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv471014	chr5:61428137-61461609	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv598323	chr5:61428137-61461609	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv462202	chr5:61430431-61461609	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv598324	chr5:61430431-61461609	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv598325	chr5:61436505-61468051	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61435000-61441600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:61438200-61440800	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr5:61438600-61440800	Enhancers	Brain Substantia Nigra	brain
4	chr5:61438800-61440800	Enhancers	Brain Anterior Caudate	brain
5	chr5:61439000-61440800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:61439200-61441000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:61439200-61441000	Enhancers	Fetal Brain Male	brain
8	chr5:61439400-61440800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:61439400-61440800	Enhancers	NH-A	brain
10	chr5:61439400-61441000	Enhancers	NHEK	skin
11	chr5:61439400-61441200	Enhancers	HMEC	breast
12	chr5:61439600-61440800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:61439800-61440800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr5:61439800-61440800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:61439800-61440800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:61439800-61440800	Enhancers	Pancreas	Pancrea
17	chr5:61440000-61440800	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr5:61440000-61441000	Enhancers	Osteobl	bone
19	chr5:61440200-61440800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:61440200-61440800	Enhancers	Brain Cingulate Gyrus	brain
21	chr5:61440200-61440800	Enhancers	Brain Germinal Matrix	brain
22	chr5:61440400-61440800	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr5:61440400-61440800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:61440400-61440800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:61440400-61440800	Enhancers	Lung	lung
26	chr5:61440400-61441200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr5:61440600-61440800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:61440600-61441000	Enhancers	Esophagus	oesophagus

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