Variant report

Variant	rs6479389
Chromosome Location	chr9:94716442-94716443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr9:94716420-94716570	HEK293	kidney:	n/a	n/a
2	CTCF	chr9:94716400-94716550	GM12873	blood:	n/a	n/a
3	CTCF	chr9:94716400-94716550	HEEpiC	esophagus:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:94712364..94714252-chr9:94715571..94717814,2	MCF-7	breast:
2	chr9:94711196..94714012-chr9:94715764..94719304,3	K562	blood:
3	chr9:94708402..94710475-chr9:94715730..94717686,2	K562	blood:
4	chr9:94714238..94717195-chr9:94796671..94799619,2	MCF-7	breast:
5	chr9:94714221..94717070-chr9:94719717..94722305,2	K562	blood:

No data

Variant related genes	Relation type
ROR2	TF binding region
ENSG00000169071	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10116249	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10118072	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10124760	0.95[EUR][1000 genomes]
rs10125384	0.86[EUR][1000 genomes]
rs10125466	0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs10512220	0.88[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10733743	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10739925	0.86[JPT][hapmap]
rs10761137	0.84[CEU][hapmap]
rs10761138	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10761143	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs10820931	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12340044	0.88[CEU][hapmap];0.91[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1316268	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1609292	0.84[CEU][hapmap]
rs1881389	0.83[ASW][hapmap]
rs1881391	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1892268	0.84[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1919100	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2297568	0.91[ASW][hapmap];0.88[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs2312739	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2895201	0.88[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3847308	0.82[CEU][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6479385	0.82[EUR][1000 genomes]
rs6479386	0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs6479387	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs6479388	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479400	0.88[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6479402	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7020136	0.84[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7023075	0.87[MEX][hapmap]
rs7034357	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7034363	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7037255	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7038017	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7041193	0.91[ASW][hapmap];0.88[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7042102	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7047326	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7048699	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7848874	0.88[ASW][hapmap];0.88[CEU][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.84[EUR][1000 genomes]
rs7848987	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7850309	0.83[EUR][1000 genomes]
rs7852032	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7859689	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7862779	0.86[EUR][1000 genomes]
rs7863167	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7867072	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7869504	0.84[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7871444	0.88[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9774945	0.92[CEU][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.83[EUR][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	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
2	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
3	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv831653	chr9:94692454-94867542	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6479389	ZNF484	cis	parietal	SCAN
rs6479389	C9orf170	cis	cerebellum	SCAN
rs6479389	ZNF484	cis	cerebellum	SCAN
rs6479389	LOC100128076	cis	lymphoblastoid	seeQTL
rs6479389	SPTLC1	cis	parietal	SCAN
rs6479389	OMD	cis	cerebellum	SCAN
rs6479389	CDK20	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94711200-94717000	Weak transcription	Fetal Heart	heart
2	chr9:94713400-94716800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr9:94713400-94720200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:94713400-94720600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:94713600-94717200	Weak transcription	Fetal Lung	lung
6	chr9:94713600-94717200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr9:94713800-94717000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr9:94714200-94716600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:94714800-94716600	Weak transcription	K562	blood
10	chr9:94714800-94717200	Weak transcription	Adipose Nuclei	Adipose
11	chr9:94714800-94717200	Weak transcription	Pancreas	Pancrea
12	chr9:94715000-94716800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr9:94715600-94716600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:94715600-94717600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr9:94716000-94717400	Enhancers	Esophagus	oesophagus
16	chr9:94716000-94717400	Enhancers	Stomach Mucosa	stomach
17	chr9:94716400-94717000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:94716400-94717000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr9:94716400-94717600	Enhancers	Gastric	stomach

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