Variant report

Variant	rs12499016
Chromosome Location	chr4:54030457-54030458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10517291	0.86[CHB][hapmap]
rs10517292	0.86[CHB][hapmap]
rs11133246	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11133247	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11929903	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11939189	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11947928	0.81[AMR][1000 genomes]
rs12108246	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12503963	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12505661	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12507228	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12512359	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12640471	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12646150	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12647441	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12650397	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17082453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17082476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17082504	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17082529	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17082565	1.00[CHB][hapmap]
rs17082581	1.00[CHB][hapmap]
rs1987028	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2001881	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2128103	0.86[CHB][hapmap]
rs34019927	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4299650	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4419530	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4421047	0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4515221	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4529117	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4864451	0.86[CHB][hapmap]
rs4864453	1.00[CHB][hapmap]
rs4864747	1.00[CHB][hapmap]
rs6554095	0.86[CHB][hapmap]
rs6826467	1.00[CHB][hapmap]
rs72624192	0.84[AMR][1000 genomes]
rs72624193	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72624194	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73143456	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73143458	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73143484	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs751265	1.00[CHB][hapmap]
rs7688646	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7696426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9761301	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12499016	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54004200-54052200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:54007200-54030600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr4:54010200-54034600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr4:54011600-54030600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:54011600-54052200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:54011800-54031600	Weak transcription	Pancreas	Pancrea
7	chr4:54018000-54035800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:54019400-54042600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:54026400-54030600	Weak transcription	Primary T cells from cord blood	blood
10	chr4:54026600-54038800	Weak transcription	Primary B cells from cord blood	blood
11	chr4:54028600-54039400	Weak transcription	NHDF-Ad	bronchial
12	chr4:54029400-54039400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:54029600-54030600	Weak transcription	Aorta	Aorta
14	chr4:54029800-54031800	Weak transcription	Right Atrium	heart
15	chr4:54029800-54034400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:54030000-54031600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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