Variant report

Variant	rs12509915
Chromosome Location	chr4:165994160-165994161
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	chr4:165993791-165995534	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000273097	TF binding region

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10021320	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10027850	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10745250	0.81[ASN][1000 genomes]
rs11731682	0.82[LWK][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap]
rs28450893	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28493629	0.89[AFR][1000 genomes]
rs28594328	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28673499	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28698808	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4470585	0.81[AFR][1000 genomes]
rs4478139	0.82[EUR][1000 genomes]
rs4538438	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4554024	0.85[EUR][1000 genomes]
rs4643773	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs7671851	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7683991	0.83[LWK][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap]
rs9999037	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026152	chr4:165622244-166027447	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv537336	chr4:165622244-166027447	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv533191	chr4:165879671-166171638	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv1835468	chr4:165969625-166023258	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
8	esv1840053	chr4:165969625-166023258	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
9	nsv881168	chr4:165975122-166196438	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:165979000-166005600	Weak transcription	Pancreas	Pancrea
2	chr4:165979200-165995000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr4:165980400-166000400	Weak transcription	Brain Angular Gyrus	brain
4	chr4:165980600-166005800	Weak transcription	Aorta	Aorta
5	chr4:165980600-166007000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr4:165981000-165996800	Weak transcription	Brain Hippocampus Middle	brain
7	chr4:165981000-165997400	Weak transcription	Brain Anterior Caudate	brain
8	chr4:165981000-165999000	Weak transcription	Brain Substantia Nigra	brain
9	chr4:165982000-166000400	Weak transcription	Ovary	ovary
10	chr4:165982200-166000400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr4:165985000-166007200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:165990600-166007000	Weak transcription	Right Ventricle	heart
13	chr4:165990800-166026600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr4:165991400-166000600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:165991600-165996000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:165991600-166008400	Weak transcription	Colon Smooth Muscle	Colon
17	chr4:165993200-165999800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:165993200-166000000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr4:165993600-166007000	Weak transcription	Fetal Lung	lung
20	chr4:165993800-165994200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:165993800-165995400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr4:165994000-165994200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:165994000-165994200	Enhancers	Fetal Intestine Large	intestine
24	chr4:165994000-165994400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:165994000-165994400	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr4:165994000-165994600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:165994000-165994600	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr4:165994000-165994600	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr4:165994000-165995400	Enhancers	Fetal Heart	heart
30	chr4:165994000-165995400	Enhancers	Fetal Intestine Small	intestine
31	chr4:165994000-165997000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr4:165994000-165999400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr4:165994000-165999600	Weak transcription	Primary B cells from cord blood	blood
34	chr4:165994000-166000200	Weak transcription	Primary T cells fromperipheralblood	blood

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