Variant report

Variant	rs2501925
Chromosome Location	chr9:79003413-79003414
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:79002107..79003757-chr9:79007780..79009963,2	MCF-7	breast:
2	chr9:79003083..79006280-chr9:79008607..79011361,3	K562	blood:
3	chr9:78991796..78994850-chr9:78999374..79004024,5	K562	blood:
4	chr9:79002425..79005766-chr9:79008607..79011361,4	K562	blood:

Variant related genes	Relation type
ENSG00000135002	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10121699	0.84[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs10124695	0.81[ASN][1000 genomes]
rs10869767	0.96[ASN][1000 genomes]
rs10869773	0.93[ASN][1000 genomes]
rs11144864	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.95[ASN][1000 genomes]
rs11144865	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs11144866	0.82[ASN][1000 genomes]
rs11144871	0.99[ASN][1000 genomes]
rs11144880	0.95[ASN][1000 genomes]
rs11144887	0.82[YRI][hapmap]
rs12057052	0.82[ASN][1000 genomes]
rs12344941	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs13295433	0.93[ASN][1000 genomes]
rs13302654	0.93[ASN][1000 genomes]
rs1535845	0.81[ASN][1000 genomes]
rs1961995	0.86[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2002423	0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2251604	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2377639	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2377640	0.88[YRI][hapmap]
rs2490572	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs2490573	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2490574	0.81[ASN][1000 genomes]
rs2490576	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2490579	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2490583	0.86[ASN][1000 genomes]
rs2490584	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2490586	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2501920	0.81[ASN][1000 genomes]
rs2501922	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2501923	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2501927	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2501928	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2501930	0.86[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2501932	0.81[ASN][1000 genomes]
rs2501933	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2501935	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35837300	0.84[ASN][1000 genomes]
rs3739729	0.99[ASN][1000 genomes]
rs4372070	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4745541	0.97[ASN][1000 genomes]
rs4745544	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs509326	0.81[EUR][1000 genomes]
rs6560515	0.88[YRI][hapmap]
rs6560517	0.93[ASN][1000 genomes]
rs6560522	0.90[JPT][hapmap]
rs7023191	0.88[YRI][hapmap]
rs7847608	0.84[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7849239	0.93[ASN][1000 genomes]
rs785936	0.83[GIH][hapmap]
rs7861089	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78986600-79008400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:78987600-79007800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:78988200-79008400	Weak transcription	Brain Substantia Nigra	brain
4	chr9:78988200-79008400	Weak transcription	Fetal Heart	heart
5	chr9:78988600-79007800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:78988600-79008200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:78988800-79006000	Weak transcription	Brain Angular Gyrus	brain
8	chr9:78988800-79007200	Weak transcription	Brain Hippocampus Middle	brain
9	chr9:78988800-79008400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr9:78990000-79005400	Weak transcription	Small Intestine	intestine
11	chr9:78990200-79007800	Weak transcription	Fetal Brain Male	brain
12	chr9:78990200-79008400	Weak transcription	Right Ventricle	heart
13	chr9:78990400-79008200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr9:78990400-79008400	Weak transcription	Fetal Kidney	kidney
15	chr9:78990600-79005600	Weak transcription	K562	blood
16	chr9:78990600-79008400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr9:78990600-79008400	Weak transcription	Fetal Lung	lung
18	chr9:78990600-79008400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr9:78990800-79008400	Weak transcription	NHLF	lung
20	chr9:78992200-79008600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:78994200-79005200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr9:78995200-79007600	Weak transcription	Gastric	stomach
23	chr9:78995200-79007600	Weak transcription	HMEC	breast
24	chr9:78995200-79007600	Weak transcription	NHEK	skin
25	chr9:78995200-79008400	Weak transcription	Stomach Mucosa	stomach
26	chr9:78995200-79008600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:78996000-79008400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr9:78997000-79007600	Weak transcription	Lung	lung
29	chr9:78997600-79005800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr9:78997600-79008400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr9:78997800-79003600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr9:78997800-79004200	Strong transcription	Liver	Liver
33	chr9:78997800-79004200	Strong transcription	Fetal Thymus	thymus
34	chr9:78997800-79004400	Strong transcription	Primary B cells from cord blood	blood
35	chr9:78997800-79004400	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr9:78997800-79008400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr9:78998000-79003800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr9:78998000-79004400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr9:78998400-79004200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr9:78998400-79004200	Strong transcription	Adipose Nuclei	Adipose
41	chr9:78998400-79008400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr9:78998600-79004200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr9:78998800-79003600	Strong transcription	Primary hematopoietic stem cells	blood
44	chr9:78998800-79007800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr9:78998800-79008600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr9:78999000-79004000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr9:78999000-79004200	Strong transcription	Primary T cells from cord blood	blood
48	chr9:78999000-79004200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr9:78999000-79004200	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr9:78999000-79004200	Strong transcription	Rectal Mucosa Donor 31	rectum

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