Variant report

Variant	rs4957798
Chromosome Location	chr5:108444554-108444555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10040959	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10043540	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs10056058	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10063845	1.00[CEU][hapmap];0.84[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10070411	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10085093	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10477944	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10477945	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10477946	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10477947	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10477948	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10477949	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10477952	0.85[EUR][1000 genomes]
rs17450345	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[ASN][1000 genomes]
rs17450387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17473391	1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[YRI][hapmap];0.81[EUR][1000 genomes]
rs17534626	0.83[EUR][1000 genomes]
rs2195944	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2217649	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2416198	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2416200	0.82[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28699553	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3816024	0.91[CHD][hapmap]
rs4957567	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4957799	1.00[CHB][hapmap]
rs55930293	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55953478	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56227556	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57196331	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59337218	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6872780	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73779027	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73779130	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73779135	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9285864	0.90[CEU][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9326759	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9326760	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9326762	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830443	chr5:108326491-108496723	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv882692	chr5:108391660-108474166	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882693	chr5:108391660-108502493	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv882694	chr5:108391660-108524416	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv4953	chr5:108443905-108488747	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4957798	EFNA5	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108422800-108444800	Weak transcription	Left Ventricle	heart
2	chr5:108435600-108446800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr5:108441400-108445400	Enhancers	Fetal Heart	heart
4	chr5:108441600-108447400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:108441600-108455600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:108441800-108455600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:108442000-108445000	Weak transcription	Brain Anterior Caudate	brain
8	chr5:108442000-108446800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:108442000-108497400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:108442400-108449000	Weak transcription	Pancreas	Pancrea
11	chr5:108442800-108445200	Weak transcription	Osteobl	bone
12	chr5:108442800-108446000	Weak transcription	HSMM	muscle
13	chr5:108442800-108455600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:108444200-108447000	Weak transcription	HUVEC	blood vessel
15	chr5:108444200-108455600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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