Variant report

Variant	rs12499731
Chromosome Location	chr4:54129137-54129138
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10517291	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10517292	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11929903	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11939189	0.80[ASN][1000 genomes]
rs11947322	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11947928	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12108246	0.82[AMR][1000 genomes]
rs12500564	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505661	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12507228	0.81[ASN][1000 genomes]
rs12512748	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17082504	0.82[AMR][1000 genomes]
rs17082529	0.81[ASN][1000 genomes]
rs17082549	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17082565	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17082579	0.81[EUR][1000 genomes]
rs17082581	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35784764	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4299650	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4385131	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4419530	0.82[AMR][1000 genomes]
rs4421047	0.82[AMR][1000 genomes]
rs4529117	0.82[AMR][1000 genomes]
rs4864451	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864452	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4864453	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4864454	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4864747	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4864753	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6826467	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6830879	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6854446	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72498838	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73147378	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73147396	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73149212	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs751265	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7664488	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7664645	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7687029	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7688646	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9762074	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv997614	chr4:54086727-54150632	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv879013	chr4:54093717-54137228	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1008593	chr4:54120297-54207769	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv2763360	chr4:54123894-54153814	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12499731	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54101600-54129400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:54108400-54129600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:54114400-54134400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:54114400-54139600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:54114400-54144000	Weak transcription	Liver	Liver
6	chr4:54114600-54129800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:54114800-54129400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:54114800-54130000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr4:54117800-54132800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:54119600-54130400	Weak transcription	NHLF	lung
11	chr4:54122200-54139800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr4:54126600-54134200	Weak transcription	Gastric	stomach
13	chr4:54126800-54141400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:54127200-54130200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr4:54127600-54153000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr4:54128000-54129600	Weak transcription	HSMMtube	muscle
17	chr4:54128000-54134400	Weak transcription	Pancreas	Pancrea
18	chr4:54128200-54136200	Weak transcription	Thymus	Thymus
19	chr4:54128600-54132800	Weak transcription	Adipose Nuclei	Adipose

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