Variant report

Variant	rs4864753
Chromosome Location	chr4:54202878-54202879
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10517291	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10517292	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11942086	0.82[AMR][1000 genomes]
rs11947322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11947928	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12499731	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12500564	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12507723	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12512748	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17082549	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17082565	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17082579	0.84[EUR][1000 genomes]
rs17082581	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35784764	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4385131	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864451	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4864452	0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4864453	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4864454	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4864747	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6826467	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6830879	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6854446	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72498838	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73147378	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73147396	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73149212	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs751265	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7664488	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7687029	0.89[EUR][1000 genomes]
rs9762074	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4864753	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54169800-54216200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:54170600-54230600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:54172600-54215400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr4:54174200-54212600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:54180000-54212800	Weak transcription	Primary B cells from cord blood	blood
6	chr4:54187800-54212800	Weak transcription	Dnd41	blood
7	chr4:54188200-54213800	Weak transcription	Right Ventricle	heart
8	chr4:54188200-54218200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:54188200-54231200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:54188400-54205600	Weak transcription	Fetal Intestine Small	intestine
11	chr4:54188400-54212800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:54188600-54215400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr4:54189600-54212800	Weak transcription	Osteobl	bone
14	chr4:54189800-54206400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:54190000-54213800	Weak transcription	HUVEC	blood vessel
16	chr4:54192200-54212600	Weak transcription	NHDF-Ad	bronchial
17	chr4:54192200-54212800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:54193800-54203000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:54193800-54203800	Weak transcription	GM12878-XiMat	blood
20	chr4:54193800-54206200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:54193800-54212600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:54193800-54213400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:54194200-54204800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr4:54201200-54220000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:54201400-54215600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr4:54201600-54213000	Weak transcription	K562	blood
27	chr4:54201800-54215800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr4:54202000-54212800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr4:54202200-54226000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr4:54202600-54213000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:54202800-54203400	Strong transcription	Primary T cells from cord blood	blood

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