Variant report

Variant	rs12501430
Chromosome Location	chr4:57109453-57109454
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	GATA3	chr4:57109286-57109660	SH-SY5Y	brain:	n/a	chr4:57109471-57109479
2	GATA2	chr4:57108988-57109636	SH-SY5Y	brain:	n/a	chr4:57109471-57109479

Variant related genes	Relation type
KIAA1211	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12506535	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12506712	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1471472	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17086510	0.82[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17086524	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4865074	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4865076	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4865077	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4865078	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4865079	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4865080	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4865081	0.95[JPT][hapmap];0.89[YRI][hapmap]
rs4865083	0.95[JPT][hapmap]
rs55705732	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6846642	0.89[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7686913	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	esv3415289	chr4:57063312-57236755	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57090400-57129000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:57095800-57117200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:57098800-57158400	Weak transcription	Fetal Brain Female	brain
4	chr4:57103400-57112200	Weak transcription	Pancreas	Pancrea
5	chr4:57105200-57110000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr4:57106800-57112000	Weak transcription	Brain Germinal Matrix	brain
7	chr4:57107000-57110400	Weak transcription	Small Intestine	intestine
8	chr4:57107400-57148400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:57107800-57111200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:57107800-57124400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:57108000-57114400	Enhancers	HepG2	liver
12	chr4:57108000-57114600	Enhancers	Fetal Intestine Large	intestine
13	chr4:57108000-57114600	Enhancers	Fetal Intestine Small	intestine
14	chr4:57108400-57110800	Weak transcription	Stomach Mucosa	stomach
15	chr4:57108800-57111000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:57108800-57113000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr4:57109000-57111000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:57109000-57111600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr4:57109200-57110800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:57109400-57112000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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