Variant report

Variant	rs13131404
Chromosome Location	chr4:512828-512829
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	POLR2A	chr4:512817-514016	GM12892	blood:	n/a	n/a
2	POLR2A	chr4:512796-513894	GM12891	blood:	n/a	n/a
3	POLR2A	chr4:512771-514448	GM12891	blood:	n/a	n/a
4	POLR2A	chr4:512727-514450	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:512537-513488	K562	blood:	n/a	n/a
6	POLR2A	chr4:512420-514445	GM12892	blood:	n/a	n/a
7	POLR2A	chr4:512607-513309	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:507598..511513-chr4:511712..515475,4	K562	blood:
2	chr4:507254..511513-chr4:511820..516333,6	K562	blood:
3	chr4:511646..516203-chr4:516278..519159,6	K562	blood:

Variant related genes	Relation type
PIGG	TF binding region
ENSG00000174227	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10029096	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10029104	0.84[JPT][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1127410	0.85[CEU][hapmap]
rs1135945	0.94[ASW][hapmap];0.90[CHD][hapmap]
rs11931500	0.85[CEU][hapmap]
rs11938226	0.85[CEU][hapmap]
rs12719770	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13114024	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13114026	0.85[CEU][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs13115344	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.81[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13124714	0.85[CEU][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13136656	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13150531	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28609510	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34872561	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35270677	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35334779	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35956476	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4324510	0.92[CEU][hapmap]
rs4365672	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4380466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4488886	0.91[CEU][hapmap]
rs4499656	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4504200	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616693	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4624610	0.86[GIH][hapmap];0.88[JPT][hapmap]
rs57834329	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6818642	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6822767	0.82[ASW][hapmap]
rs6827438	0.85[CEU][hapmap]
rs6847066	0.84[CEU][hapmap]
rs7660555	0.85[CEU][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7666226	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7666425	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7668455	0.85[CEU][hapmap]
rs7671228	0.83[EUR][1000 genomes]
rs7672868	0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7678962	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7692313	0.85[CEU][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1001899	chr4:68809-517736	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532703	chr4:72447-614414	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
7	nsv532704	chr4:85040-628550	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv1010829	chr4:147570-547070	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv536970	chr4:147570-547070	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
11	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
12	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats 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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:493600-520000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:494400-521400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr4:494400-531000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:494400-533200	Strong transcription	Placenta	Placenta
5	chr4:494400-534600	Weak transcription	Fetal Heart	heart
6	chr4:494600-525600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:494600-532000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:494600-533000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:494600-533200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:494600-533200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:494800-513200	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr4:494800-513400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:494800-513600	Strong transcription	Primary B cells from peripheral blood	blood
14	chr4:495000-533000	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:495200-533000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:495200-534000	Strong transcription	Fetal Stomach	stomach
17	chr4:495400-513600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:496400-533000	Strong transcription	Fetal Brain Female	brain
19	chr4:496800-532000	Strong transcription	Dnd41	blood
20	chr4:498400-513800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:498800-513000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:499400-513600	Strong transcription	Brain Germinal Matrix	brain
23	chr4:499600-526600	Strong transcription	Primary B cells from cord blood	blood
24	chr4:503000-530600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr4:503000-531600	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr4:503200-530800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr4:503600-532000	Strong transcription	Primary T cells from cord blood	blood
28	chr4:503800-532800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:504600-526200	Weak transcription	Stomach Mucosa	stomach
30	chr4:505400-514800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:506400-513200	Strong transcription	Fetal Muscle Trunk	muscle
32	chr4:506400-524800	Strong transcription	Lung	lung
33	chr4:506400-525400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:506400-533200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:506600-513000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:506600-513600	Strong transcription	Adipose Nuclei	Adipose
37	chr4:506600-522200	Strong transcription	Spleen	Spleen
38	chr4:506600-522400	Strong transcription	Ovary	ovary
39	chr4:506600-531800	Strong transcription	Thymus	Thymus
40	chr4:506600-532200	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr4:506600-532800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:506600-533200	Strong transcription	Fetal Intestine Large	intestine
43	chr4:506600-533400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:506600-533600	Strong transcription	Liver	Liver
45	chr4:506800-513000	Strong transcription	Gastric	stomach
46	chr4:506800-513000	Strong transcription	HSMMtube	muscle
47	chr4:506800-513200	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr4:506800-513200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr4:506800-513400	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr4:506800-513400	Strong transcription	Rectal Smooth Muscle	rectum

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