Variant report

Variant	rs959619
Chromosome Location	chr6:114163460-114163461
allele	A/G
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	JUND	chr6:114163219-114163978	SK-N-SH	brain:	n/a	n/a
2	POU2F2	chr6:114163335-114163618	GM12878	blood:	n/a	chr6:114163516-114163528
3	GATA3	chr6:114163298-114164269	SK-N-SH	brain:	n/a	n/a
4	TEAD4	chr6:114163198-114163972	SK-N-SH	brain:	n/a	n/a
5	FOSL2	chr6:114163237-114163916	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr6:114163104-114164024	SK-N-SH	brain:	n/a	n/a
7	FOXM1	chr6:114163290-114164142	SK-N-SH	brain:	n/a	n/a
8	PBX3	chr6:114163156-114164037	SK-N-SH	brain:	n/a	n/a
9	EP300	chr6:114163163-114164121	SK-N-SH	brain:	n/a	n/a
10	TEAD4	chr6:114163175-114163963	SK-N-SH	brain:	n/a	n/a
11	BATF	chr6:114163399-114163662	GM12878	blood:	n/a	n/a
12	TCF12	chr6:114163175-114164135	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr6:114163293-114163779	SK-N-SH	brain:	n/a	n/a
14	GATA3	chr6:114163118-114164295	SK-N-SH	brain:	n/a	n/a
15	RUNX3	chr6:114163270-114163687	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:114163368-114163516	SK-N-SH	brain:	n/a	n/a
17	POU2F2	chr6:114163378-114163583	GM12878	blood:	n/a	chr6:114163516-114163528
18	RUNX3	chr6:114163364-114163669	GM12878	blood:	n/a	n/a
19	PBX3	chr6:114163273-114163985	SK-N-SH	brain:	n/a	n/a
20	POU2F2	chr6:114163331-114163629	GM12891	blood:	n/a	chr6:114163516-114163528
21	EP300	chr6:114163289-114163698	SK-N-SH_RA	brain:	n/a	n/a
22	EP300	chr6:114163248-114163998	SK-N-SH	brain:	n/a	n/a
23	NFIC	chr6:114163230-114163969	SK-N-SH	brain:	n/a	n/a
24	JUND	chr6:114163212-114163967	SK-N-SH	brain:	n/a	n/a
25	EP300	chr6:114163330-114163567	SK-N-SH_RA	brain:	n/a	n/a
26	PAX5	chr6:114163336-114163624	GM12878	blood:	n/a	n/a
27	POU2F2	chr6:114163356-114163632	GM12891	blood:	n/a	chr6:114163516-114163528

Variant related genes	Relation type
ENSG00000231912	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10872108	0.86[ASN][1000 genomes]
rs10872109	0.93[EUR][1000 genomes]
rs11153443	0.86[ASN][1000 genomes]
rs11153446	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11153447	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11153450	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11757604	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12202789	0.86[ASN][1000 genomes]
rs12205735	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1462381	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1980375	0.95[CHB][hapmap];0.90[CHD][hapmap];0.87[TSI][hapmap]
rs2348532	0.80[ASN][1000 genomes]
rs4034906	0.82[ASN][1000 genomes]
rs4089883	0.85[ASN][1000 genomes]
rs4945974	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6909293	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6918413	0.83[ASN][1000 genomes]
rs6919507	0.85[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.84[LWK][hapmap];0.88[MKK][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]
rs6942382	0.81[ASN][1000 genomes]
rs7764655	0.86[ASN][1000 genomes]
rs7773346	0.80[ASN][1000 genomes]
rs9372379	0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[TSI][hapmap]
rs9372380	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9384884	0.89[ASN][1000 genomes]
rs9400673	0.89[ASN][1000 genomes]
rs954620	0.95[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021774	chr6:114063971-114407280	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv538422	chr6:114063971-114407280	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3363275	chr6:114101331-114302866	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs959619	GTF3C6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114162000-114169600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:114162800-114164000	Enhancers	NHDF-Ad	bronchial
3	chr6:114163200-114164000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:114163400-114163800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:114163400-114164000	Enhancers	HSMM	muscle
6	chr6:114163400-114164200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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