Variant report

Variant	rs7459539
Chromosome Location	chr8:95783824-95783825
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:95698786..95700613-chr8:95783550..95785146,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241003	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10100724	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10100860	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11785908	0.86[AMR][1000 genomes]
rs11996148	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs13248163	0.84[ASN][1000 genomes]
rs13249787	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13252877	0.95[ASN][1000 genomes]
rs13262041	0.88[AFR][1000 genomes]
rs13271653	0.80[AMR][1000 genomes]
rs13277564	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13279429	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34152155	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs34179463	0.82[ASN][1000 genomes]
rs35050854	0.82[ASN][1000 genomes]
rs35123111	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs35249319	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs35296683	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs35353222	0.88[AFR][1000 genomes]
rs35769195	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35799116	0.86[ASN][1000 genomes]
rs35866149	0.84[ASN][1000 genomes]
rs35937656	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3924073	0.86[ASN][1000 genomes]
rs3924074	0.86[ASN][1000 genomes]
rs4236829	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4236830	0.86[AMR][1000 genomes]
rs4268099	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs4332100	0.81[EUR][1000 genomes]
rs4351387	0.84[ASN][1000 genomes]
rs4377930	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4398879	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4448241	0.80[EUR][1000 genomes]
rs4478541	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4545065	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4548145	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4734286	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4734288	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4734289	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4735318	0.84[ASN][1000 genomes]
rs4735323	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4735325	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6415569	0.82[JPT][hapmap]
rs6415570	0.82[JPT][hapmap]
rs6471489	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6471491	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6985400	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6988572	0.80[EUR][1000 genomes]
rs6988791	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6992217	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6996787	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6999453	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7006999	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes]
rs7014120	1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7017149	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs71532330	0.84[ASN][1000 genomes]
rs7818257	0.84[ASN][1000 genomes]
rs7832492	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7837249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7459539	LOC203107	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95733000-95784400	Weak transcription	Esophagus	oesophagus
2	chr8:95733000-95803800	Weak transcription	Psoas Muscle	Psoas
3	chr8:95733000-95805200	Weak transcription	Colonic Mucosa	Colon
4	chr8:95733200-95805000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr8:95733400-95784800	Weak transcription	Small Intestine	intestine
6	chr8:95733600-95809400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr8:95733800-95806400	Weak transcription	Fetal Brain Male	brain
8	chr8:95734200-95784600	Weak transcription	Brain Angular Gyrus	brain
9	chr8:95735400-95787800	Weak transcription	Hela-S3	cervix
10	chr8:95740800-95799000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr8:95744000-95790800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr8:95752400-95809200	Weak transcription	NHLF	lung
13	chr8:95752600-95784200	Weak transcription	A549	lung
14	chr8:95752600-95793400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr8:95752600-95805600	Weak transcription	NHEK	skin
16	chr8:95753600-95791200	Weak transcription	Primary B cells from cord blood	blood
17	chr8:95761800-95784600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr8:95761800-95785400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr8:95761800-95803600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr8:95762200-95793600	Weak transcription	Stomach Mucosa	stomach
21	chr8:95766200-95788400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr8:95767600-95795000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr8:95772400-95784600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr8:95773200-95804800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr8:95773600-95809400	Weak transcription	HSMMtube	muscle
26	chr8:95773800-95802600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr8:95774000-95788000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr8:95774000-95791200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr8:95774000-95798000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr8:95774200-95792000	Strong transcription	Fetal Intestine Large	intestine
31	chr8:95774400-95791800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr8:95774400-95792000	Strong transcription	Fetal Intestine Small	intestine
33	chr8:95774400-95792000	Strong transcription	Fetal Stomach	stomach
34	chr8:95774400-95792200	Strong transcription	Fetal Muscle Leg	muscle
35	chr8:95774800-95799800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr8:95774800-95803200	Weak transcription	Fetal Heart	heart
37	chr8:95775200-95786200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr8:95776200-95797800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr8:95776200-95803800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr8:95776800-95786600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr8:95777000-95787800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr8:95777200-95785200	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr8:95777200-95789600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr8:95777200-95792200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr8:95777400-95785200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr8:95777400-95804000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr8:95777600-95788000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr8:95777800-95785600	Strong transcription	Dnd41	blood
49	chr8:95777800-95789200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr8:95778000-95785000	Strong transcription	Primary T cells fromperipheralblood	blood

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