Variant report

Variant	rs1464565
Chromosome Location	chr15:30202751-30202752
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1001877	0.86[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs12592270	0.82[ASN][1000 genomes]
rs12594438	0.84[ASN][1000 genomes]
rs12594461	0.84[ASN][1000 genomes]
rs1357386	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1357387	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1357388	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1403354	0.85[AFR][1000 genomes]
rs1464564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522640	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522643	0.83[ASN][1000 genomes]
rs1522790	0.85[AFR][1000 genomes]
rs1522791	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1522792	0.86[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs1522794	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1533860	0.98[ASN][1000 genomes]
rs1533861	0.82[CHD][hapmap]
rs1631472	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1632356	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1718974	0.85[AFR][1000 genomes]
rs1718977	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718985	0.85[ASN][1000 genomes]
rs1718986	0.86[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs1718987	0.85[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs1718988	0.85[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs1718989	0.85[ASN][1000 genomes]
rs1718990	0.86[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs1718991	0.85[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs1718993	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1718997	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1718998	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1718999	0.85[ASN][1000 genomes]
rs1719032	0.85[AFR][1000 genomes]
rs1719033	0.85[AFR][1000 genomes]
rs1719036	0.85[AFR][1000 genomes]
rs1719040	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719041	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719332	0.84[AFR][1000 genomes]
rs1719337	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1719338	0.92[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1719341	0.85[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs1719343	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1719345	0.85[ASN][1000 genomes]
rs1719348	0.86[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs1719349	0.84[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs1719350	0.85[ASN][1000 genomes]
rs1719351	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1719352	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1719353	0.85[ASN][1000 genomes]
rs1719354	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1719358	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1719359	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1719360	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1719361	0.86[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap];0.85[ASN][1000 genomes]
rs1879895	0.86[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap]
rs2103056	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2253906	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2461657	0.85[ASN][1000 genomes]
rs2948554	0.85[AFR][1000 genomes]
rs2948555	0.85[ASN][1000 genomes]
rs34866689	0.85[ASN][1000 genomes]
rs4503741	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4779461	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4779672	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4779673	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4779674	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4779675	0.86[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs4779676	0.93[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4779677	0.84[ASN][1000 genomes]
rs867024	0.85[AFR][1000 genomes]
rs867025	0.85[AFR][1000 genomes]
rs939976	0.85[ASN][1000 genomes]
rs939977	0.84[ASN][1000 genomes]
rs939978	0.84[ASN][1000 genomes]
rs939979	0.85[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.85[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
rs1464565	TJP1	cis	cerebellum	SCAN

Chromatin state (count:21 , 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	chr15:30196600-30203200	Weak transcription	Left Ventricle	heart
4	chr15:30196600-30204200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr15:30196600-30205600	Weak transcription	Fetal Lung	lung
6	chr15:30197400-30204200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:30197400-30204200	Weak transcription	Brain Substantia Nigra	brain
8	chr15:30198200-30204000	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:30200200-30203200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr15:30200200-30204200	Weak transcription	Brain Angular Gyrus	brain
11	chr15:30200800-30205200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:30201600-30203200	Enhancers	Hela-S3	cervix
13	chr15:30201600-30203400	Enhancers	Colon Smooth Muscle	Colon
14	chr15:30201800-30203200	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr15:30201800-30204000	Enhancers	Fetal Heart	heart
16	chr15:30202000-30202800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr15:30202000-30203000	Weak transcription	Right Atrium	heart
18	chr15:30202000-30205600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr15:30202200-30203000	Weak transcription	Brain Anterior Caudate	brain
20	chr15:30202200-30206600	Weak transcription	Right Ventricle	heart
21	chr15:30202600-30202800	Enhancers	Stomach Smooth Muscle	stomach

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