Variant report

Variant	rs1953616
Chromosome Location	chr13:92214699-92214700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:92049894..92051792-chr13:92212556..92214796,2	K562	blood:
2	chr13:92214626..92216806-chr13:92217477..92220350,2	K562	blood:
3	chr13:92208317..92211893-chr13:92214191..92217203,4	K562	blood:
4	chr13:92064271..92067451-chr13:92214102..92216956,3	K562	blood:
5	chr13:92127298..92129816-chr13:92213589..92216245,2	K562	blood:
6	chr13:92000817..92003388-chr13:92213282..92215654,2	K562	blood:
7	chr13:92007765..92009366-chr13:92214136..92216197,2	K562	blood:

Variant related genes	Relation type
ENSG00000179399	Chromatin interaction
ENSG00000215417	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs12583138	0.89[ASN][1000 genomes]
rs1336208	0.87[CEU][hapmap];0.89[CHB][hapmap];0.82[EUR][1000 genomes]
rs1336219	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1336220	0.98[ASN][1000 genomes]
rs1414714	0.95[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs1414715	0.95[CHD][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.92[ASN][1000 genomes]
rs1414716	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs1572433	0.98[ASN][1000 genomes]
rs16946173	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17483	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2065849	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2065851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2065852	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2184728	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2351871	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4143764	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4359314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4402419	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.98[ASN][1000 genomes]
rs4771841	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.97[ASN][1000 genomes]
rs4773638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs493369	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs6492554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659614	0.83[CEU][hapmap]
rs7319303	0.95[ASN][1000 genomes]
rs7324772	0.95[ASN][1000 genomes]
rs7332002	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7490394	0.89[ASN][1000 genomes]
rs7982049	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7983224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7984663	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7993829	0.95[CHB][hapmap]
rs870112	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs870113	1.00[ASN][1000 genomes]
rs9301734	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9301738	0.98[ASN][1000 genomes]
rs945532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs945533	0.80[LWK][hapmap];0.80[MKK][hapmap];0.81[YRI][hapmap]
rs9515937	0.91[ASN][1000 genomes]
rs9515939	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.98[ASN][1000 genomes]
rs9515943	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs9515944	0.92[ASN][1000 genomes]
rs9523346	0.88[CHB][hapmap];0.82[AMR][1000 genomes]
rs9523348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs9523351	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9523352	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9523358	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs9523366	0.97[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.94[ASN][1000 genomes]
rs9583946	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9589295	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs9589296	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9589297	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[ASN][1000 genomes]
rs9589298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9589299	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042947	chr13:91571040-92416897	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
2	nsv541871	chr13:91571040-92416897	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
3	esv1803618	chr13:91669587-92277699	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1945 gene(s)	inside rSNPs	diseases
4	nsv1049382	chr13:92024240-92521180	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv541873	chr13:92024240-92521180	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv562714	chr13:92056911-92304974	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1036860	chr13:92061347-92291771	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv562715	chr13:92061878-92299609	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1041168	chr13:92062057-92301861	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv949582	chr13:92062331-92301861	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1041762	chr13:92065459-92267509	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv541874	chr13:92065459-92267509	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv529091	chr13:92065460-92267510	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1045465	chr13:92065659-92267370	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv541875	chr13:92065659-92267370	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv531890	chr13:92065660-92267369	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv1040707	chr13:92072034-92302281	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv1045421	chr13:92075673-92283600	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv541876	chr13:92075673-92283600	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv530635	chr13:92084151-92280466	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv1045669	chr13:92111663-92245308	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv541878	chr13:92111663-92245308	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv562716	chr13:92128694-92250454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv562717	chr13:92135345-92250454	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	nsv1040709	chr13:92173603-92318362	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
26	esv3392280	chr13:92193762-92217325	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1953616	GPC5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:92211000-92215800	Weak transcription	Right Atrium	heart

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