Variant report

Variant	rs7029809
Chromosome Location	chr9:94542262-94542263
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94534777..94536619-chr9:94540454..94542317,2	MCF-7	breast:
2	chr9:94509113..94511832-chr9:94540924..94543887,2	K562	blood:
3	chr9:94541932..94544615-chr9:94547110..94550430,3	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10992081	0.86[ASN][1000 genomes]
rs10992082	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs10992091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992093	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992094	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10992096	1.00[ASN][1000 genomes]
rs10992097	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10992099	0.88[ASN][1000 genomes]
rs10992105	0.82[ASN][1000 genomes]
rs1406201	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2312731	0.82[ASN][1000 genomes]
rs34466526	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4237216	0.82[ASN][1000 genomes]
rs4467997	0.82[LWK][hapmap]
rs4744097	0.80[LWK][hapmap]
rs7025400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029673	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041425	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71494476	0.85[AFR][1000 genomes]
rs72744489	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73651504	0.85[AFR][1000 genomes]
rs7860482	0.91[ASW][hapmap];0.81[LWK][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes]
rs7862819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7863557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7872865	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7029809	ASPN	cis	parietal	SCAN
rs7029809	NXNL2	cis	parietal	SCAN
rs7029809	S1PR3	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94533000-94542800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:94533000-94543600	Weak transcription	Right Atrium	heart
3	chr9:94533400-94549600	Weak transcription	Colonic Mucosa	Colon
4	chr9:94533600-94545400	Enhancers	Stomach Smooth Muscle	stomach
5	chr9:94534400-94546800	Weak transcription	Fetal Kidney	kidney
6	chr9:94536000-94543200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr9:94536000-94543600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:94536200-94544600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr9:94537000-94543400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:94537800-94543400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:94537800-94545000	Weak transcription	Fetal Intestine Small	intestine
12	chr9:94537800-94546000	Weak transcription	Gastric	stomach
13	chr9:94538000-94548800	Weak transcription	Esophagus	oesophagus
14	chr9:94538600-94543200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:94538800-94543400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr9:94538800-94543400	Weak transcription	Ovary	ovary
17	chr9:94539000-94543200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr9:94539200-94543400	Weak transcription	Fetal Heart	heart
19	chr9:94539400-94543400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr9:94539600-94543600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr9:94539600-94543800	Weak transcription	Fetal Stomach	stomach
22	chr9:94539800-94542600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:94539800-94543400	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:94540600-94546000	Weak transcription	K562	blood
25	chr9:94540800-94543200	Weak transcription	Fetal Lung	lung
26	chr9:94540800-94543600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:94540800-94545000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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