Variant report

Variant	rs13115344
Chromosome Location	chr4:515489-515490
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	chr4:515476-516027	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:514891..517080-chr4:677730..679355,2	MCF-7	breast:
2	chr4:507254..511513-chr4:511820..516333,6	K562	blood:
3	chr4:511646..516203-chr4:516278..519159,6	K562	blood:
4	chr4:515315..517143-chr4:524895..527185,2	K562	blood:

Variant related genes	Relation type
PIGG	TF binding region
ENSG00000174227	Chromatin interaction
ENSG00000169026	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10029096	0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10029104	0.83[JPT][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11248023	0.81[EUR][1000 genomes]
rs1127410	0.80[TSI][hapmap]
rs1135945	0.94[ASW][hapmap];0.90[CHD][hapmap]
rs11931500	0.82[EUR][1000 genomes]
rs11931543	0.80[EUR][1000 genomes]
rs11931692	0.81[EUR][1000 genomes]
rs11933478	0.81[EUR][1000 genomes]
rs11934538	0.80[EUR][1000 genomes]
rs11934549	0.82[EUR][1000 genomes]
rs11936515	0.80[EUR][1000 genomes]
rs11936548	0.80[EUR][1000 genomes]
rs11936717	0.80[EUR][1000 genomes]
rs11938183	0.81[EUR][1000 genomes]
rs11938226	0.81[EUR][1000 genomes]
rs11940796	0.80[EUR][1000 genomes]
rs11940914	0.80[EUR][1000 genomes]
rs11946204	0.81[EUR][1000 genomes]
rs12719770	0.85[CEU][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13106068	0.80[EUR][1000 genomes]
rs13114024	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13114026	0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs13124714	0.88[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13131404	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]
rs13136656	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13141560	0.81[EUR][1000 genomes]
rs13150531	1.00[ASW][hapmap];0.90[CHD][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28609510	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28624264	0.80[EUR][1000 genomes]
rs28684815	0.80[EUR][1000 genomes]
rs3211083	0.81[EUR][1000 genomes]
rs34247702	0.80[EUR][1000 genomes]
rs34327839	0.81[EUR][1000 genomes]
rs34584074	0.81[EUR][1000 genomes]
rs34623004	0.81[EUR][1000 genomes]
rs34872561	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35270677	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35334779	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35479345	0.80[EUR][1000 genomes]
rs35629431	0.81[EUR][1000 genomes]
rs35956476	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4324510	0.85[CEU][hapmap]
rs4365672	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4380466	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4488886	0.83[CEU][hapmap]
rs4499656	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4504200	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616693	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4624610	0.82[GIH][hapmap];0.88[JPT][hapmap]
rs55983970	0.80[EUR][1000 genomes]
rs57834329	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6818642	0.92[CEU][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6822767	0.82[ASW][hapmap]
rs73072173	0.81[EUR][1000 genomes]
rs73072175	0.81[EUR][1000 genomes]
rs7660555	0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7666226	1.00[ASW][hapmap];0.90[CHD][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7666425	1.00[ASW][hapmap];0.90[CHD][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7671228	0.87[EUR][1000 genomes]
rs7672868	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.80[TSI][hapmap];0.85[ASN][1000 genomes]
rs7678962	1.00[ASW][hapmap];0.90[CHD][hapmap];0.85[LWK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7692313	0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[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	chr4:495000-533000	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:495200-533000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:495200-534000	Strong transcription	Fetal Stomach	stomach
14	chr4:496400-533000	Strong transcription	Fetal Brain Female	brain
15	chr4:496800-532000	Strong transcription	Dnd41	blood
16	chr4:499600-526600	Strong transcription	Primary B cells from cord blood	blood
17	chr4:503000-530600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:503000-531600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr4:503200-530800	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr4:503600-532000	Strong transcription	Primary T cells from cord blood	blood
21	chr4:503800-532800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:504600-526200	Weak transcription	Stomach Mucosa	stomach
23	chr4:506400-524800	Strong transcription	Lung	lung
24	chr4:506400-525400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:506400-533200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr4:506600-522200	Strong transcription	Spleen	Spleen
27	chr4:506600-522400	Strong transcription	Ovary	ovary
28	chr4:506600-531800	Strong transcription	Thymus	Thymus
29	chr4:506600-532200	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr4:506600-532800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:506600-533200	Strong transcription	Fetal Intestine Large	intestine
32	chr4:506600-533400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:506600-533600	Strong transcription	Liver	Liver
34	chr4:506800-520200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:506800-532000	Strong transcription	Duodenum Mucosa	Duodenum
36	chr4:506800-532600	Strong transcription	Aorta	Aorta
37	chr4:506800-533000	Strong transcription	Stomach Smooth Muscle	stomach
38	chr4:506800-533200	Strong transcription	Fetal Muscle Leg	muscle
39	chr4:507200-519400	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr4:507200-520400	Strong transcription	Colonic Mucosa	Colon
41	chr4:507200-523000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr4:507200-526000	Strong transcription	NHLF	lung
43	chr4:507200-533400	Strong transcription	Brain Anterior Caudate	brain
44	chr4:507400-517600	Weak transcription	Right Atrium	heart
45	chr4:507400-520400	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr4:507400-522400	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr4:507400-533600	Strong transcription	Brain Hippocampus Middle	brain
48	chr4:507600-533200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr4:507600-533600	Strong transcription	Brain Cingulate Gyrus	brain
50	chr4:508600-532000	Strong transcription	Primary neutrophils fromperipheralblood	blood

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