Variant report

Variant	rs9409651
Chromosome Location	chr9:94498550-94498551
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94497499..94499840-chr9:94505365..94508110,2	MCF-7	breast:
2	chr9:94497979..94500430-chr9:94500591..94503129,2	K562	blood:
3	chr9:94493263..94495550-chr9:94497375..94499893,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10820900	0.80[ASN][1000 genomes]
rs3935601	0.82[TSI][hapmap]
rs3935603	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4073735	0.82[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.83[MKK][hapmap];0.87[ASN][1000 genomes]
rs4073736	0.82[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs4237215	0.89[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7031729	0.82[TSI][hapmap]
rs7855522	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7869182	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9409456	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9409457	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9409458	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9409649	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9409650	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9409652	0.81[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9409651	S1PR3	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94477200-94533000	Weak transcription	Fetal Kidney	kidney
2	chr9:94483400-94501600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr9:94483600-94504000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:94483600-94519400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:94486200-94521000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:94486800-94517400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:94487000-94502200	Weak transcription	Esophagus	oesophagus
8	chr9:94487000-94535400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:94489000-94508800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:94490400-94521000	Weak transcription	Right Atrium	heart
11	chr9:94491600-94501000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:94493200-94517400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr9:94495000-94501800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:94495600-94498800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:94496400-94499800	Strong transcription	K562	blood
16	chr9:94496600-94499800	Strong transcription	Fetal Lung	lung
17	chr9:94497200-94499000	Weak transcription	NHLF	lung
18	chr9:94497200-94499600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr9:94497200-94502400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:94497200-94502400	Weak transcription	Spleen	Spleen
21	chr9:94497200-94502600	Strong transcription	Fetal Stomach	stomach
22	chr9:94497400-94503000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:94497600-94499800	Strong transcription	Stomach Smooth Muscle	stomach
24	chr9:94497600-94503000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:94498200-94499800	Strong transcription	Fetal Intestine Small	intestine
26	chr9:94498200-94499800	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr9:94498400-94499400	Strong transcription	Fetal Intestine Large	intestine
28	chr9:94498400-94499800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:94498400-94499800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr9:94498400-94499800	Genic enhancers	Colon Smooth Muscle	Colon
31	chr9:94498400-94499800	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr9:94498400-94499800	Strong transcription	Fetal Muscle Leg	muscle
33	chr9:94498400-94499800	Strong transcription	Gastric	stomach
34	chr9:94498400-94499800	Strong transcription	Ovary	ovary
35	chr9:94498400-94500400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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