Variant report

Variant	rs726519
Chromosome Location	chr14:25522269-25522270
allele	A/C
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	POLR2A	chr14:25522142-25522295	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:25516181..25518992-chr14:25521102..25522786,2	K562	blood:

Variant related genes	Relation type
STXBP6	TF binding region
ENSG00000168952	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11626133	0.90[ASN][1000 genomes]
rs11626436	0.94[JPT][hapmap]
rs11627702	0.89[ASN][1000 genomes]
rs17185453	0.88[JPT][hapmap]
rs17257668	0.88[JPT][hapmap]
rs17257780	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs1886055	0.88[JPT][hapmap]
rs1952494	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1952495	0.93[ASN][1000 genomes]
rs1958381	0.85[YRI][hapmap]
rs1958384	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1958386	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2332464	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7142942	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7151656	0.97[ASN][1000 genomes]
rs7151785	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs8007052	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.98[ASN][1000 genomes]
rs8020392	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv901504	chr14:25184210-25646203	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv901509	chr14:25398571-25743484	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv901510	chr14:25476170-25526309	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
6	nsv901511	chr14:25505085-25588029	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs726519	STXBP6	cis	parietal	SCAN
rs726519	PRMT5	cis	parietal	SCAN
rs726519	SALL2	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25520000-25522400	Enhancers	Placenta Amnion	Placenta Amnion
2	chr14:25520200-25522400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
3	chr14:25520200-25522600	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr14:25520200-25525200	Weak transcription	Brain Substantia Nigra	brain
5	chr14:25520200-25525600	Weak transcription	Brain Angular Gyrus	brain
6	chr14:25520400-25522400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
7	chr14:25520400-25525600	Weak transcription	Brain Anterior Caudate	brain
8	chr14:25520400-25525600	Weak transcription	Brain Hippocampus Middle	brain
9	chr14:25520800-25525000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr14:25520800-25525000	Weak transcription	HSMM	muscle
11	chr14:25520800-25525200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr14:25520800-25525600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr14:25520800-25526000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr14:25521200-25522400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr14:25521200-25524200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr14:25521200-25524200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr14:25521400-25522400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
18	chr14:25521600-25534400	Weak transcription	Pancreas	Pancrea
19	chr14:25522000-25522800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr14:25522000-25526200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr14:25522200-25522400	Enhancers	H9 Cell Line	embryonic stem cell

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