Variant report

Variant	rs4699959
Chromosome Location	chr5:59875933-59875934
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10043291	0.82[CHB][hapmap]
rs10058456	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs10939860	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs10939862	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11739724	0.84[ASN][1000 genomes]
rs11740327	0.87[CHB][hapmap]
rs11741754	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11948543	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs11951503	0.82[ASN][1000 genomes]
rs11951950	0.90[ASN][1000 genomes]
rs11952735	0.82[ASN][1000 genomes]
rs11955398	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11959922	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs12514253	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs12515025	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs12517174	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs12517207	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs12522801	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1379114	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1379115	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1379116	0.85[CHB][hapmap]
rs1456742	0.86[CHB][hapmap]
rs1456743	0.86[CHB][hapmap]
rs1562235	0.88[ASN][1000 genomes]
rs17387940	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1867702	0.80[ASN][1000 genomes]
rs1870014	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs187481	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1992612	0.86[CHB][hapmap]
rs2061250	0.90[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs206789	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2409791	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2409792	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs249070	0.85[ASN][1000 genomes]
rs2591636	0.82[ASN][1000 genomes]
rs286153	0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs286154	0.87[CHB][hapmap]
rs286155	0.82[ASN][1000 genomes]
rs286156	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs286158	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2898287	0.88[ASN][1000 genomes]
rs3857236	0.90[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs3958943	0.89[ASN][1000 genomes]
rs4277863	0.86[CHB][hapmap]
rs4307050	0.90[CEU][hapmap]
rs4326096	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4515250	1.00[CEU][hapmap]
rs4524466	0.91[CHB][hapmap]
rs4700378	0.84[ASN][1000 genomes]
rs4700379	0.86[ASN][1000 genomes]
rs4700380	0.83[ASN][1000 genomes]
rs5012862	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55768631	0.87[ASN][1000 genomes]
rs56137970	0.89[ASN][1000 genomes]
rs56166952	0.83[ASN][1000 genomes]
rs62372964	0.89[ASN][1000 genomes]
rs6449478	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6449480	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6449484	1.00[CEU][hapmap]
rs6449493	0.86[CHB][hapmap]
rs6877561	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6896680	1.00[CEU][hapmap]
rs6896942	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs755077	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7720233	0.86[CHB][hapmap]
rs7725028	0.92[AMR][1000 genomes]
rs7730342	0.86[CHB][hapmap]
rs9942410	0.91[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4699959	ELOVL7	Cis_1M	lymphoblastoid	RTeQTL
rs4699959	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59873000-59908600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:59873000-59908800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:59873200-59881200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr5:59873200-59911000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:59874600-59889600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:59874600-59890400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:59875400-59895800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:59875400-59895800	Weak transcription	Fetal Thymus	thymus
9	chr5:59875400-59899400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:59875400-59911000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:59875600-59876200	Weak transcription	Dnd41	blood
12	chr5:59875600-59878800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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