Variant report

Variant	rs4380521
Chromosome Location	chr4:19535243-19535244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10003702	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10006103	0.87[ASN][1000 genomes]
rs10006299	0.87[ASN][1000 genomes]
rs10009772	0.90[ASN][1000 genomes]
rs10012861	0.90[ASN][1000 genomes]
rs10015294	0.83[ASN][1000 genomes]
rs10025775	0.87[ASN][1000 genomes]
rs10028337	0.90[ASN][1000 genomes]
rs10031579	0.96[ASN][1000 genomes]
rs10032188	0.90[ASN][1000 genomes]
rs10032629	0.83[ASN][1000 genomes]
rs10034324	0.87[ASN][1000 genomes]
rs10222803	0.87[ASN][1000 genomes]
rs10222907	0.87[ASN][1000 genomes]
rs10222971	0.86[ASN][1000 genomes]
rs10223045	0.87[ASN][1000 genomes]
rs10470799	0.81[ASN][1000 genomes]
rs11933898	0.85[ASN][1000 genomes]
rs11940870	0.88[CHB][hapmap]
rs11941599	0.90[ASN][1000 genomes]
rs11941815	0.88[ASN][1000 genomes]
rs11944084	0.91[ASN][1000 genomes]
rs11945412	0.90[ASN][1000 genomes]
rs11946126	0.88[ASN][1000 genomes]
rs1388148	0.81[ASN][1000 genomes]
rs16868608	0.83[ASN][1000 genomes]
rs28392619	0.87[ASN][1000 genomes]
rs28406392	0.90[ASN][1000 genomes]
rs28445313	0.80[ASN][1000 genomes]
rs28468581	0.83[ASN][1000 genomes]
rs28505527	0.90[ASN][1000 genomes]
rs28506946	0.88[ASN][1000 genomes]
rs28584356	0.81[ASN][1000 genomes]
rs28612466	0.80[ASN][1000 genomes]
rs28625215	0.87[ASN][1000 genomes]
rs28649908	0.90[ASN][1000 genomes]
rs28654609	0.87[ASN][1000 genomes]
rs28662302	0.90[ASN][1000 genomes]
rs28675174	0.83[ASN][1000 genomes]
rs28698715	0.87[ASN][1000 genomes]
rs28713269	0.90[ASN][1000 genomes]
rs28749929	0.87[ASN][1000 genomes]
rs28809022	0.83[ASN][1000 genomes]
rs28834385	0.87[ASN][1000 genomes]
rs28849735	0.83[ASN][1000 genomes]
rs28861473	0.87[ASN][1000 genomes]
rs4472135	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4541506	0.90[ASN][1000 genomes]
rs4572879	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4637398	0.90[ASN][1000 genomes]
rs59810064	0.90[ASN][1000 genomes]
rs60069867	0.90[ASN][1000 genomes]
rs60284344	0.83[ASN][1000 genomes]
rs61359326	0.83[ASN][1000 genomes]
rs62296707	0.90[ASN][1000 genomes]
rs62296709	0.90[ASN][1000 genomes]
rs62298737	0.83[ASN][1000 genomes]
rs6837423	0.90[ASN][1000 genomes]
rs73092965	0.83[ASN][1000 genomes]
rs73092970	0.83[ASN][1000 genomes]
rs73092977	0.83[ASN][1000 genomes]
rs73092981	0.83[ASN][1000 genomes]
rs73092983	0.83[ASN][1000 genomes]
rs73092984	0.83[ASN][1000 genomes]
rs73097402	0.90[ASN][1000 genomes]
rs73099604	0.90[ASN][1000 genomes]
rs73099613	0.90[ASN][1000 genomes]
rs73099658	0.90[ASN][1000 genomes]
rs73099698	0.83[ASN][1000 genomes]
rs73101116	0.83[ASN][1000 genomes]
rs73101119	0.83[ASN][1000 genomes]
rs73110735	0.81[ASN][1000 genomes]
rs9291404	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs982066	0.81[ASN][1000 genomes]
rs982067	0.81[ASN][1000 genomes]
rs9990468	0.90[ASN][1000 genomes]
rs9994751	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998589	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878732	chr4:19172031-19660947	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv878733	chr4:19335464-19928602	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv878734	chr4:19474680-19598710	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv461286	chr4:19488871-19709795	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv593786	chr4:19488871-19709795	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv593788	chr4:19521736-19535243	Enhancers Weak transcription	lncRNA	n/a	inside rSNPs	diseases
7	nsv593789	chr4:19521736-19541708	Enhancers Weak transcription	lncRNA	n/a	inside rSNPs	diseases
8	esv1830015	chr4:19523949-19545872	Enhancers Flanking Active TSS Weak transcription Active TSS	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4380521	SLC9A5	trans	lymphoblastoid	seeQTL
rs4380521	INTS4	trans	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:19533000-19536600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr4:19533200-19536400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:19534400-19535800	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:19535200-19535600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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