Variant report

Variant	rs12433619
Chromosome Location	chr14:71679203-71679204
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	EBF1	chr14:71678699-71679248	GM12878	blood:	n/a	chr14:71679110-71679120 chr14:71679111-71679120 chr14:71678879-71678889 chr14:71679111-71679120
2	RUNX3	chr14:71678779-71679207	GM12878	blood:	n/a	n/a
3	PAX5	chr14:71678996-71679254	GM12878	blood:	n/a	chr14:71679064-71679083
4	REST	chr14:71678965-71679250	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000258517	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10129258	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10133468	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10136305	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs10139524	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10141056	0.80[AMR][1000 genomes]
rs10145569	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs10149204	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10873245	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11158897	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11158899	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11850277	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12432518	0.92[ASN][1000 genomes]
rs12433847	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12436768	0.92[ASN][1000 genomes]
rs12884828	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs12896453	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2158532	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3742845	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4899391	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6574008	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs6574010	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8012457	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8013728	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8023180	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1036929	chr14:71469148-71683412	Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1044090	chr14:71496198-71780026	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv832827	chr14:71676178-71833519	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12433619	PCNX	cis	cerebellum	SCAN
rs12433619	PCNX	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71661200-71679400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:71674000-71680400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr14:71676400-71679800	Enhancers	Brain Cingulate Gyrus	brain
4	chr14:71677400-71679400	Weak transcription	Spleen	Spleen
5	chr14:71678400-71679400	Enhancers	Brain Angular Gyrus	brain
6	chr14:71678400-71679600	Enhancers	Brain Anterior Caudate	brain
7	chr14:71678800-71679800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr14:71678800-71679800	Enhancers	GM12878-XiMat	blood
9	chr14:71678800-71681000	Enhancers	Dnd41	blood
10	chr14:71679000-71679400	Enhancers	Brain Hippocampus Middle	brain
11	chr14:71679000-71679400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr14:71679000-71679600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr14:71679000-71679800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:71679000-71679800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr14:71679000-71679800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr14:71679000-71679800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr14:71679200-71679400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr14:71679200-71679800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr14:71679200-71679800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr14:71679200-71679800	Enhancers	NHEK	skin

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