Variant report

Variant	rs12498657
Chromosome Location	chr4:120262866-120262867
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10000544	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10003567	0.81[CEU][hapmap]
rs10006192	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10006259	0.81[CEU][hapmap]
rs10012408	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10013042	0.81[CEU][hapmap]
rs10015579	0.88[AMR][1000 genomes]
rs10015965	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10016241	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10022448	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10023641	0.80[EUR][1000 genomes]
rs10025925	0.83[AMR][1000 genomes]
rs10028773	0.83[AMR][1000 genomes]
rs10518300	0.81[CEU][hapmap]
rs11098501	0.81[CEU][hapmap]
rs11732686	0.94[CEU][hapmap]
rs12502393	0.81[AMR][1000 genomes]
rs12502524	0.83[AMR][1000 genomes]
rs12506421	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12506445	0.81[AMR][1000 genomes]
rs12506487	0.83[AMR][1000 genomes]
rs12507565	0.81[CEU][hapmap]
rs12510133	0.83[AMR][1000 genomes]
rs12511640	0.81[CEU][hapmap]
rs12711071	0.81[CEU][hapmap]
rs1511017	0.81[CEU][hapmap]
rs1511025	0.81[CEU][hapmap]
rs1546503	0.80[CEU][hapmap]
rs17009144	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1814813	0.80[AMR][1000 genomes]
rs1980025	0.81[CEU][hapmap]
rs1980026	0.80[CEU][hapmap]
rs2136911	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28369518	0.83[AMR][1000 genomes]
rs28396837	0.83[AMR][1000 genomes]
rs28437684	0.81[AMR][1000 genomes]
rs28546691	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28551750	0.84[AMR][1000 genomes]
rs28572003	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28589345	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28599836	0.85[AMR][1000 genomes]
rs28691602	0.81[AMR][1000 genomes]
rs28714087	0.81[AMR][1000 genomes]
rs28726222	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3864142	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3864144	0.83[AMR][1000 genomes]
rs4001390	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55820750	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6815291	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6838009	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6838457	0.82[AMR][1000 genomes]
rs714899	0.81[CEU][hapmap]
rs7672594	0.81[CEU][hapmap]
rs878372	0.81[CEU][hapmap]
rs907205	0.81[CEU][hapmap]
rs9991959	0.81[CEU][hapmap]
rs9995716	0.86[AMR][1000 genomes]
rs9999724	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv879841	chr4:120244085-120388406	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv879842	chr4:120244085-120424087	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv2538163	chr4:120252854-120388678	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv964091	chr4:120255342-120290951	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12498657	LOC284701///FLJ14186///LOC441124///LOC641693///LOC642788///LOC653056	cis	uninvolved skin	skin_eQTL
rs12498657	RP11-33B1.1	cis	Whole Blood	GTEx
rs12498657	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs12498657	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs12498657	RP11-33B1.1	cis	Nerve Tibial	GTEx
rs12498657	RP11-33B1.1	cis	Esophagus Mucosa	GTEx
rs12498657	RP11-384K6.6	cis	Whole Blood	GTEx
rs12498657	RP11-33B1.1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120262200-120264600	Weak transcription	HepG2	liver

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