Variant report

Variant	rs1719332
Chromosome Location	chr15:30205176-30205177
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1357386	0.86[LWK][hapmap];0.82[AFR][1000 genomes]
rs1357387	0.82[AFR][1000 genomes]
rs1357388	0.82[AFR][1000 genomes]
rs1403354	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464564	0.84[AFR][1000 genomes]
rs1464565	0.84[AFR][1000 genomes]
rs1522790	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522794	0.82[AFR][1000 genomes]
rs1533861	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs1546748	0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs1554528	0.89[AFR][1000 genomes]
rs1618252	0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs1631472	0.81[AFR][1000 genomes]
rs1718974	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718976	0.89[AFR][1000 genomes]
rs1718978	0.89[AFR][1000 genomes]
rs1718980	0.86[AFR][1000 genomes]
rs1718981	0.86[AFR][1000 genomes]
rs1718993	0.81[AFR][1000 genomes]
rs1719032	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1719033	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719036	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719040	0.82[AFR][1000 genomes]
rs1719041	0.82[AFR][1000 genomes]
rs1719338	0.82[AFR][1000 genomes]
rs1719339	0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs1719351	0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs1719352	0.83[AFR][1000 genomes]
rs1719354	0.82[AFR][1000 genomes]
rs1719358	0.81[AFR][1000 genomes]
rs1719360	0.82[AFR][1000 genomes]
rs2103056	0.81[AFR][1000 genomes]
rs2948554	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4779461	0.81[CHD][hapmap]
rs4779674	0.82[CHD][hapmap]
rs59177696	0.88[ASN][1000 genomes]
rs61213468	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs867024	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867025	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv995038	chr15:29744279-30366124	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1038495	chr15:29825859-30351687	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv542293	chr15:29825859-30351687	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	esv2422463	chr15:30003189-30215336	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv903754	chr15:30023454-30382120	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv903755	chr15:30036085-30351434	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv482572	chr15:30118905-30304529	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv456739	chr15:30178614-30366247	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv568716	chr15:30178614-30366247	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv431371	chr15:30193316-31012794	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1719332	TJP1	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:30190000-30206600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:30193400-30209800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:30196600-30205600	Weak transcription	Fetal Lung	lung
4	chr15:30200800-30205200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:30202000-30205600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr15:30202200-30206600	Weak transcription	Right Ventricle	heart
7	chr15:30203400-30205200	Weak transcription	Colon Smooth Muscle	Colon
8	chr15:30203600-30206400	Weak transcription	Right Atrium	heart
9	chr15:30204000-30206600	Enhancers	Brain Hippocampus Middle	brain
10	chr15:30204200-30206600	Enhancers	Brain Substantia Nigra	brain
11	chr15:30204200-30207200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:30204200-30207400	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr15:30204200-30207800	Enhancers	Brain Angular Gyrus	brain
14	chr15:30204400-30205200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr15:30204400-30206600	Weak transcription	Left Ventricle	heart
16	chr15:30204600-30206800	Enhancers	Brain Anterior Caudate	brain
17	chr15:30204600-30207200	Enhancers	NH-A	brain
18	chr15:30204600-30207400	Enhancers	Brain Cingulate Gyrus	brain
19	chr15:30205000-30205400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr15:30205000-30207000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:30205000-30207200	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr15:30205000-30207400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:30205000-30207600	Enhancers	Fetal Heart	heart

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