Variant report

Variant	rs12719140
Chromosome Location	chr5:111602603-111602604
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	GATA2	chr5:111602595-111603334	SH-SY5Y	brain:	n/a	chr5:111603004-111603014 chr5:111603097-111603108

Variant related genes	Relation type
EPB41L4A	TF binding region

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

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

rs_ID	r²[population]
rs10478074	0.85[CHB][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10478076	0.95[ASN][1000 genomes]
rs12652766	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12655450	0.95[ASN][1000 genomes]
rs12656841	0.90[ASN][1000 genomes]
rs13358904	0.85[CHB][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28620667	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34819608	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35005258	0.89[ASN][1000 genomes]
rs36049225	0.89[ASN][1000 genomes]
rs4323272	0.85[CHB][hapmap];0.90[ASN][1000 genomes]
rs4635975	0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4958024	0.89[YRI][hapmap];0.94[ASN][1000 genomes]
rs4958026	0.96[ASN][1000 genomes]
rs4958027	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4958028	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4958029	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57970031	0.95[ASN][1000 genomes]
rs59775924	0.95[ASN][1000 genomes]
rs60823180	0.96[ASN][1000 genomes]
rs61475230	0.97[ASN][1000 genomes]
rs61535569	0.96[ASN][1000 genomes]
rs62364080	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6879361	0.94[ASN][1000 genomes]
rs7715255	0.90[YRI][hapmap];0.96[ASN][1000 genomes]
rs7716479	0.98[ASN][1000 genomes]
rs9326851	0.92[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599367	chr5:110924280-111602713	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv531291	chr5:111497440-111756788	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv599371	chr5:111519018-111676755	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111564600-111609600	Weak transcription	Pancreas	Pancrea
2	chr5:111568600-111609600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:111584800-111605600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:111585800-111606000	Weak transcription	Spleen	Spleen
5	chr5:111586600-111626400	Weak transcription	Gastric	stomach
6	chr5:111590400-111609600	Weak transcription	Psoas Muscle	Psoas
7	chr5:111590400-111628200	Weak transcription	Aorta	Aorta
8	chr5:111590600-111605800	Weak transcription	Right Ventricle	heart
9	chr5:111590800-111617000	Weak transcription	Left Ventricle	heart
10	chr5:111590800-111617200	Weak transcription	Esophagus	oesophagus
11	chr5:111590800-111618200	Weak transcription	Right Atrium	heart
12	chr5:111591400-111606600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:111593400-111605600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:111594000-111606200	Weak transcription	HUVEC	blood vessel
15	chr5:111594000-111611600	Weak transcription	Placenta	Placenta
16	chr5:111594800-111605800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr5:111594800-111615000	Weak transcription	Fetal Kidney	kidney
18	chr5:111595400-111604600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr5:111596000-111605800	Weak transcription	Hela-S3	cervix
20	chr5:111596200-111603400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr5:111598600-111606200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr5:111599000-111603200	Weak transcription	Adipose Nuclei	Adipose
23	chr5:111599800-111603400	Enhancers	Fetal Heart	heart
24	chr5:111600800-111612800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:111601800-111612600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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