Variant report

Variant	rs3935601
Chromosome Location	chr9:94508700-94508701
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	chr9:94508551..94510877-chr9:94514167..94515784,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs3935603	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4467996	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs4493962	0.81[ASN][1000 genomes]
rs7031729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7047937	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7855522	0.91[GIH][hapmap];0.82[TSI][hapmap]
rs7869182	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9409458	0.82[TSI][hapmap]
rs9409651	0.82[TSI][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3935601	S1PR3	cis	cerebellum	SCAN
rs3935601	OMD	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94477200-94533000	Weak transcription	Fetal Kidney	kidney
2	chr9:94483600-94519400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:94486200-94521000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:94486800-94517400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:94487000-94535400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr9:94489000-94508800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:94490400-94521000	Weak transcription	Right Atrium	heart
8	chr9:94493200-94517400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr9:94499400-94509400	Weak transcription	Fetal Intestine Large	intestine
10	chr9:94499600-94517200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:94499800-94508800	Weak transcription	K562	blood
12	chr9:94499800-94517000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr9:94499800-94520400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr9:94499800-94522800	Weak transcription	Gastric	stomach
15	chr9:94499800-94523200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:94501000-94515800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:94502800-94516600	Weak transcription	Fetal Intestine Small	intestine
18	chr9:94503200-94515800	Weak transcription	Fetal Lung	lung
19	chr9:94503800-94508800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:94504200-94509200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:94504400-94509000	Weak transcription	Osteobl	bone
22	chr9:94504400-94509200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:94504400-94517400	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:94504600-94509200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:94504600-94509600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:94504600-94512800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:94506200-94523600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr9:94508200-94509000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:94508400-94510200	Strong transcription	Fetal Stomach	stomach
30	chr9:94508600-94509000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr9:94508600-94510000	Enhancers	Ovary	ovary

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