Variant report

Variant	rs7039620
Chromosome Location	chr9:94535632-94535633
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	chr9:94534777..94536619-chr9:94540454..94542317,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10512217	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10992086	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10992087	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10992088	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10992089	1.00[ASN][1000 genomes]
rs10992100	1.00[ASW][hapmap];0.88[LWK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs12235606	0.88[ASN][1000 genomes]
rs12235611	0.98[ASN][1000 genomes]
rs12237459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12238428	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs16907741	0.98[ASN][1000 genomes]
rs16907754	0.98[ASN][1000 genomes]
rs16907761	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16907764	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34854279	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4467997	1.00[ASW][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes]
rs4595186	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4744097	1.00[ASW][hapmap];0.85[JPT][hapmap];0.90[LWK][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes]
rs4744098	0.95[AFR][1000 genomes]
rs60099576	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7026175	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73511102	1.00[ASN][1000 genomes]
rs7855073	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs7855079	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045332	chr9:94352661-94656016	Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv531631	chr9:94373847-94633213	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv6612	chr9:94490644-94535738	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1036176	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv540171	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7039620	GADD45G	cis	cerebellum	SCAN
rs7039620	ZNF484	cis	parietal	SCAN
rs7039620	C9orf89	cis	parietal	SCAN
rs7039620	C9orf79	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94527600-94538800	Weak transcription	K562	blood
2	chr9:94529400-94539800	Enhancers	Colon Smooth Muscle	Colon
3	chr9:94532200-94537000	Enhancers	Duodenum Smooth Muscle	Duodenum
4	chr9:94532200-94539200	Enhancers	Fetal Heart	heart
5	chr9:94532800-94536000	Enhancers	HSMMtube	muscle
6	chr9:94532800-94536400	Enhancers	Fetal Lung	lung
7	chr9:94533000-94542800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:94533000-94543600	Weak transcription	Right Atrium	heart
9	chr9:94533400-94535800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:94533400-94537600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:94533400-94537600	Enhancers	Rectal Smooth Muscle	rectum
12	chr9:94533400-94549600	Weak transcription	Colonic Mucosa	Colon
13	chr9:94533600-94545400	Enhancers	Stomach Smooth Muscle	stomach
14	chr9:94534000-94536600	Enhancers	Placenta	Placenta
15	chr9:94534200-94537400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr9:94534200-94538200	Genic enhancers	Fetal Stomach	stomach
17	chr9:94534400-94546800	Weak transcription	Fetal Kidney	kidney
18	chr9:94534600-94537600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:94534600-94538000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:94534600-94538800	Weak transcription	Spleen	Spleen
21	chr9:94534600-94539400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:94534800-94536200	Enhancers	Fetal Intestine Large	intestine
23	chr9:94534800-94537400	Weak transcription	Gastric	stomach
24	chr9:94534800-94537600	Weak transcription	Ovary	ovary
25	chr9:94535000-94536200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:94535000-94536400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr9:94535000-94538000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:94535000-94538600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:94535000-94539400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:94535200-94536000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:94535200-94536200	Weak transcription	Fetal Intestine Small	intestine
32	chr9:94535200-94536600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr9:94535400-94536000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:94535400-94536000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr9:94535400-94536000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:94535400-94536400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:94535600-94536000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr9:94535600-94536200	Enhancers	H1 Cell Line	embryonic stem cell
39	chr9:94535600-94536200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr9:94535600-94536200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr9:94535600-94536200	Enhancers	Esophagus	oesophagus
42	chr9:94535600-94536200	Enhancers	Placenta Amnion	Placenta Amnion
43	chr9:94535600-94537600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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