Variant report

Variant	rs4744097
Chromosome Location	chr9:94543365-94543366
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94509113..94511832-chr9:94540924..94543887,2	K562	blood:
2	chr9:94542440..94546170-chr9:94710664..94713670,3	K562	blood:
3	chr9:94541932..94544615-chr9:94547110..94550430,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169071	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10512217	0.85[JPT][hapmap]
rs10992086	0.85[JPT][hapmap]
rs10992087	0.85[JPT][hapmap]
rs10992088	0.85[JPT][hapmap]
rs10992100	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12237459	0.85[JPT][hapmap]
rs16907761	0.85[JPT][hapmap]
rs16907764	0.85[JPT][hapmap]
rs34854279	0.90[AFR][1000 genomes]
rs4467997	1.00[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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4595186	0.85[JPT][hapmap]
rs4744098	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60099576	0.82[AFR][1000 genomes]
rs7021529	0.95[EUR][1000 genomes]
rs7026175	1.00[ASW][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs7029809	0.80[LWK][hapmap]
rs7039620	1.00[ASW][hapmap];0.85[JPT][hapmap];0.90[LWK][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes]
rs7855073	0.96[YRI][hapmap]
rs7855079	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	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
6	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
rs4744097	S1PR3	cis	parietal	SCAN
rs4744097	C9orf79	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94533000-94543600	Weak transcription	Right Atrium	heart
2	chr9:94533400-94549600	Weak transcription	Colonic Mucosa	Colon
3	chr9:94533600-94545400	Enhancers	Stomach Smooth Muscle	stomach
4	chr9:94534400-94546800	Weak transcription	Fetal Kidney	kidney
5	chr9:94536000-94543600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr9:94536200-94544600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr9:94537000-94543400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr9:94537800-94543400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:94537800-94545000	Weak transcription	Fetal Intestine Small	intestine
10	chr9:94537800-94546000	Weak transcription	Gastric	stomach
11	chr9:94538000-94548800	Weak transcription	Esophagus	oesophagus
12	chr9:94538800-94543400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr9:94538800-94543400	Weak transcription	Ovary	ovary
14	chr9:94539200-94543400	Weak transcription	Fetal Heart	heart
15	chr9:94539400-94543400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr9:94539600-94543600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:94539600-94543800	Weak transcription	Fetal Stomach	stomach
18	chr9:94539800-94543400	Weak transcription	Colon Smooth Muscle	Colon
19	chr9:94540600-94546000	Weak transcription	K562	blood
20	chr9:94540800-94543600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:94540800-94545000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:94542800-94543600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:94543200-94543400	Enhancers	H9 Cell Line	embryonic stem cell
24	chr9:94543200-94543600	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr9:94543200-94544400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:94543200-94544400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr9:94543200-94544600	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr9:94543200-94545400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr9:94543200-94546600	Enhancers	Fetal Lung	lung

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