Variant report

Variant	rs6478062
Chromosome Location	chr9:116858625-116858626
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr9:116858430-116858752	HEK293-T-REx	kidney:	n/a	n/a
2	CTCF	chr9:116858228-116858661	K562	blood:	n/a	n/a
3	RAD21	chr9:116858255-116858659	HepG2	liver:	n/a	chr9:116858316-116858325
4	RAD21	chr9:116858246-116858673	H1-hESC	embryonic stem cell:	n/a	chr9:116858316-116858325
5	CTCF	chr9:116858580-116858730	GM12873	blood:	n/a	n/a
6	CTCF	chr9:116858480-116858630	GM12872	blood:	n/a	n/a
7	CTCF	chr9:116858326-116858632	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr9:116858500-116858650	HCM	heart:	n/a	n/a
9	CTCF	chr9:116858560-116858710	HVMF	connective:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:116856264..116859004-chr9:116870407..116871935,2	MCF-7	breast:

Variant related genes	Relation type
KIF12	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10116075	0.80[EUR][1000 genomes]
rs10119159	0.81[CEU][hapmap]
rs10982059	0.80[EUR][1000 genomes]
rs13284299	0.84[ASN][1000 genomes]
rs13285436	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1465657	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs1465659	0.84[ASN][1000 genomes]
rs1560539	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs1886128	0.94[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1982048	0.81[CEU][hapmap]
rs1982049	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs2093785	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2116403	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs2251700	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2285055	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2418265	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs2761691	0.81[CEU][hapmap]
rs3810929	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4979338	0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs6478063	0.84[ASN][1000 genomes]
rs6478064	0.84[ASN][1000 genomes]
rs6478065	0.83[ASN][1000 genomes]
rs6478066	0.83[ASN][1000 genomes]
rs7029198	0.84[ASN][1000 genomes]
rs7036734	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs7037166	0.81[ASN][1000 genomes]
rs7040719	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs7045137	0.83[ASN][1000 genomes]
rs7853169	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7854030	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	esv2422396	chr9:116792944-117354862	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
3	nsv466514	chr9:116810890-116867054	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv615222	chr9:116810890-116867054	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	esv2422492	chr9:116811294-117366643	Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
6	esv2761285	chr9:116811897-117103268	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
7	nsv466515	chr9:116814661-116867054	Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv615223	chr9:116814661-116867054	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv528822	chr9:116815777-116867054	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv466516	chr9:116815777-116867054	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv466518	chr9:116815777-116867054	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv466519	chr9:116815777-116867054	Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
13	nsv466520	chr9:116815777-116867054	Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
14	nsv466521	chr9:116815777-116867054	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
15	nsv466522	chr9:116815777-116867054	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
16	nsv466523	chr9:116815777-116867054	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
17	nsv471319	chr9:116815777-116867054	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
18	nsv615224	chr9:116815777-116867054	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
19	nsv466524	chr9:116826842-116867054	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv466525	chr9:116826842-116867054	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	nsv615225	chr9:116826842-116867054	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	nsv870215	chr9:116842614-117070344	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	124 gene(s)	inside rSNPs	diseases
23	nsv893751	chr9:116846467-116874355	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv515856	chr9:116853797-116867054	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6478062	KIF12	cis	cerebellum	SCAN
rs6478062	KIAA0368	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116843000-116858800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:116849000-116858800	Weak transcription	HepG2	liver
3	chr9:116854800-116859600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr9:116855000-116858800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr9:116855400-116858800	Strong transcription	Gastric	stomach
6	chr9:116855400-116859800	Weak transcription	Lung	lung
7	chr9:116855400-116859800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr9:116856400-116859800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr9:116857000-116859200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr9:116857400-116859800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr9:116858200-116859400	Weak transcription	Fetal Kidney	kidney
12	chr9:116858200-116859800	Weak transcription	Liver	Liver
13	chr9:116858400-116859000	Genic enhancers	Fetal Intestine Large	intestine
14	chr9:116858400-116859400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr9:116858400-116860000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
16	chr9:116858600-116859000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:116858600-116859600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:116858600-116859600	Genic enhancers	Pancreas	Pancrea

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