Variant report

Variant	rs2490572
Chromosome Location	chr9:78987645-78987646
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:78987493..78989026-chr9:79006994..79008780,2	K562	blood:
2	chr9:78981679..78983727-chr9:78987229..78989632,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135002	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10121699	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10124695	0.87[ASN][1000 genomes]
rs10735646	0.82[CHB][hapmap]
rs11144864	0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11144865	0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11788095	0.86[ASN][1000 genomes]
rs12057052	0.94[ASN][1000 genomes]
rs13288968	0.97[ASN][1000 genomes]
rs13302654	0.85[ASN][1000 genomes]
rs1535845	0.87[ASN][1000 genomes]
rs1961995	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2002423	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2377639	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2377641	0.82[YRI][hapmap]
rs2490573	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2490574	0.94[ASN][1000 genomes]
rs2490576	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2490579	0.84[AFR][1000 genomes]
rs2490583	0.88[ASN][1000 genomes]
rs2490584	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2490586	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2501920	0.87[ASN][1000 genomes]
rs2501923	0.83[AFR][1000 genomes]
rs2501925	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs2501927	0.84[AFR][1000 genomes]
rs2501928	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2501930	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2501932	0.96[ASN][1000 genomes]
rs2501933	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2501935	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2501937	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2501938	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2501939	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2501940	0.87[ASN][1000 genomes]
rs2501942	0.87[ASN][1000 genomes]
rs4372070	1.00[JPT][hapmap]
rs4745544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4745545	0.83[ASN][1000 genomes]
rs4745546	0.82[ASN][1000 genomes]
rs6560520	0.90[EUR][1000 genomes]
rs6560521	0.90[EUR][1000 genomes]
rs6560522	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs7847608	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2490572	RFK	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78969200-78988000	Weak transcription	Aorta	Aorta
2	chr9:78980400-78990000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:78981600-78988000	Weak transcription	K562	blood
4	chr9:78983800-78989000	Enhancers	Fetal Lung	lung
5	chr9:78984400-78989600	Enhancers	Hela-S3	cervix
6	chr9:78984600-78993200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:78984800-78987800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr9:78984800-78989800	Weak transcription	Left Ventricle	heart
9	chr9:78985000-78988000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:78985000-78988000	Weak transcription	Fetal Muscle Leg	muscle
11	chr9:78985000-78989000	Weak transcription	Pancreas	Pancrea
12	chr9:78985000-78989600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr9:78985000-78989600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:78985000-78989800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr9:78985600-78989600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr9:78986000-78990400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:78986400-78988000	Enhancers	Colonic Mucosa	Colon
18	chr9:78986600-78988000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:78986600-78988600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr9:78986600-79008400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr9:78986800-78987800	Enhancers	Duodenum Mucosa	Duodenum
22	chr9:78986800-78988200	Enhancers	Stomach Smooth Muscle	stomach
23	chr9:78986800-78988600	Enhancers	Osteobl	bone
24	chr9:78986800-78988800	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr9:78986800-78989000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr9:78986800-78989000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:78986800-78989000	Enhancers	NH-A	brain
28	chr9:78986800-78989200	Enhancers	Ovary	ovary
29	chr9:78986800-78990400	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr9:78986800-78990600	Enhancers	Liver	Liver
31	chr9:78986800-78990800	Enhancers	Fetal Intestine Large	intestine
32	chr9:78986800-78990800	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr9:78986800-78991000	Enhancers	Fetal Stomach	stomach
34	chr9:78987000-78987800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:78987000-78988000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:78987000-78988000	Weak transcription	Gastric	stomach
37	chr9:78987000-78988200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:78987000-78988200	Enhancers	Fetal Heart	heart
39	chr9:78987000-78988200	Enhancers	HSMMtube	muscle
40	chr9:78987000-78988800	Enhancers	Brain Anterior Caudate	brain
41	chr9:78987000-78989000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr9:78987000-78989000	Flanking Active TSS	A549	lung
43	chr9:78987000-78989200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr9:78987000-78989400	Weak transcription	Lung	lung
45	chr9:78987000-78990000	Enhancers	Small Intestine	intestine
46	chr9:78987000-78990200	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr9:78987000-78990600	Enhancers	Colon Smooth Muscle	Colon
48	chr9:78987000-78990600	Enhancers	Fetal Intestine Small	intestine
49	chr9:78987000-78990600	Enhancers	HepG2	liver
50	chr9:78987000-78991000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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