Variant report

Variant	rs1953559
Chromosome Location	chr14:20698298-20698299
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10131951	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs10141571	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs10498266	0.87[JPT][hapmap]
rs11851950	0.80[JPT][hapmap]
rs12432119	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap]
rs12433799	0.87[JPT][hapmap]
rs12436141	0.85[JPT][hapmap]
rs12437363	0.87[JPT][hapmap];0.82[MEX][hapmap]
rs12590453	0.81[JPT][hapmap]
rs12878196	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap]
rs12891553	0.80[JPT][hapmap]
rs12894566	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs17211285	0.80[JPT][hapmap]
rs17277207	0.87[JPT][hapmap]
rs17277221	0.80[JPT][hapmap]
rs17277228	0.80[JPT][hapmap]
rs1953556	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1953558	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1959344	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs1959347	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs28663430	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35661012	0.99[ASN][1000 genomes]
rs4981097	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4981098	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4981839	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4981844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs945462	0.95[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901299	chr14:20191869-20756887	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2751268	chr14:20203125-20716841	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv1043923	chr14:20338742-21336425	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
4	nsv541970	chr14:20338742-21336425	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
5	nsv1043938	chr14:20427182-20776276	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv541971	chr14:20427182-20776276	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	nsv1037160	chr14:20517485-20901811	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
8	nsv541974	chr14:20517485-20901811	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
9	nsv832739	chr14:20604126-20734222	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv901466	chr14:20656645-20707100	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv456144	chr14:20684277-20709118	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv563844	chr14:20684277-20709118	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv456145	chr14:20684277-20712322	Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv563845	chr14:20684277-20712322	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv1055102	chr14:20687007-20743269	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv901467	chr14:20687978-20719360	Active TSS ZNF genes & repeats Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
17	nsv1052883	chr14:20689721-20743269	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
18	nsv974433	chr14:20691427-20698541	Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	nsv916964	chr14:20691437-20716830	Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1953559	RPGRIP1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:20698000-20698400	Active TSS	Fetal Heart	heart

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