Variant report

Variant	rs526007
Chromosome Location	chr12:121085884-121085885
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:121085740-121085890	BJ	skin:	n/a	n/a
2	CTCF	chr12:121085860-121086010	GM12873	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:121085752..121087777-chr12:121138546..121140930,2	MCF-7	breast:
2	chr12:121084960..121086596-chr12:121087744..121089271,2	K562	blood:
3	chr12:121084859..121087400-chr12:121088955..121093657,4	MCF-7	breast:
4	chr12:121083460..121086406-chr12:121125581..121127490,2	K562	blood:
5	chr12:121085668..121087390-chr12:121148054..121149834,2	MCF-7	breast:
6	chr12:121079111..121082636-chr12:121084242..121087390,3	K562	blood:

No data

Variant related genes	Relation type
CABP1	TF binding region
ENSG00000157782	Chromatin interaction
ENSG00000256008	Chromatin interaction
ENSG00000175970	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1168067	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1168069	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168070	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12423417	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2461507	0.85[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2673617	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2686552	0.83[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2686555	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2859263	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs473121	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4766975	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767921	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs495265	0.92[ASN][1000 genomes]
rs496212	0.91[ASN][1000 genomes]
rs513175	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs522632	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs541619	0.82[CHB][hapmap]
rs555379	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs568489	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs569499	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs715120	0.94[ASN][1000 genomes]
rs7305821	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899557	chr12:121069201-121189116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1045923	chr12:121082203-121146219	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs526007	TAOK3	cis	parietal	SCAN
rs526007	FOXG1	trans	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121079600-121086800	Weak transcription	Right Atrium	heart
2	chr12:121084800-121086600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:121084800-121086600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr12:121085000-121086000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:121085000-121086000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr12:121085000-121086800	Weak transcription	Brain Anterior Caudate	brain
7	chr12:121085000-121086800	Weak transcription	Esophagus	oesophagus
8	chr12:121085200-121086600	Weak transcription	Primary B cells from cord blood	blood
9	chr12:121085200-121086800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:121085200-121086800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr12:121085400-121086200	Weak transcription	Brain Angular Gyrus	brain
12	chr12:121085400-121086600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:121085800-121086800	Enhancers	GM12878-XiMat	blood

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