Variant report

Variant	rs4864747
Chromosome Location	chr4:54181789-54181790
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54174793..54178568-chr4:54179278..54182842,3	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10013573	0.85[CHB][hapmap]
rs1014056	0.85[CHB][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap]
rs10517291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10517292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10517296	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs11133267	0.85[CHB][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap]
rs11929903	1.00[ASW][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs11930070	1.00[CEU][hapmap]
rs11939189	0.93[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap]
rs11947322	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11947928	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12108246	0.93[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes]
rs12499016	1.00[CHB][hapmap]
rs12499401	0.85[CHB][hapmap]
rs12499731	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12500564	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12505661	0.82[AMR][1000 genomes]
rs12512748	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13120051	0.85[CHB][hapmap]
rs13125807	0.83[CHB][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap]
rs1351514	0.85[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.82[MEX][hapmap]
rs17082453	0.85[CHB][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap]
rs17082476	0.93[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap]
rs17082504	1.00[ASW][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs17082549	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17082565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17082579	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17082581	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17082910	0.85[CHB][hapmap]
rs1987028	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs2001881	0.85[CHB][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap]
rs2128103	0.85[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap]
rs2292579	0.85[CHB][hapmap]
rs35225781	0.85[CHB][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap]
rs35784764	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3817270	0.85[CHB][hapmap]
rs3946758	0.84[CHB][hapmap]
rs4299650	0.82[AMR][1000 genomes]
rs4385131	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4419530	0.82[AMR][1000 genomes]
rs4421047	0.93[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes]
rs4529117	0.82[AMR][1000 genomes]
rs4864451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4864452	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864453	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864454	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864753	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6420001	0.85[CHB][hapmap];0.80[GIH][hapmap];0.84[MEX][hapmap]
rs6554095	0.85[CHB][hapmap]
rs6554096	0.85[CHB][hapmap]
rs6554108	0.85[CHB][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap]
rs6826467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6830879	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6854446	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72498838	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73147378	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73147396	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73149212	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs751265	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7664488	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7664645	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7684450	0.85[CHB][hapmap]
rs7687029	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7688646	1.00[ASW][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs7696426	0.85[CHB][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap]
rs9762074	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9992820	0.85[CHB][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap]
rs9997844	0.85[CHB][hapmap]

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
rs4864747	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54168200-54188000	Weak transcription	Left Ventricle	heart
2	chr4:54169200-54187800	Weak transcription	Liver	Liver
3	chr4:54169400-54187400	Weak transcription	Dnd41	blood
4	chr4:54169600-54187800	Weak transcription	Brain Angular Gyrus	brain
5	chr4:54169800-54187800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr4:54169800-54216200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr4:54170000-54183800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr4:54170000-54186800	Weak transcription	HSMM	muscle
9	chr4:54170600-54187600	Weak transcription	K562	blood
10	chr4:54170600-54230600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:54171200-54188000	Weak transcription	Esophagus	oesophagus
12	chr4:54171600-54187600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr4:54172000-54188000	Weak transcription	Pancreas	Pancrea
14	chr4:54172000-54188000	Weak transcription	HepG2	liver
15	chr4:54172200-54181800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:54172600-54215400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:54173000-54187600	Weak transcription	Brain Anterior Caudate	brain
18	chr4:54173200-54182000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr4:54173400-54186800	Weak transcription	NH-A	brain
20	chr4:54173600-54182200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:54173800-54181800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr4:54174200-54187200	Weak transcription	Adipose Nuclei	Adipose
23	chr4:54174200-54187400	Weak transcription	A549	lung
24	chr4:54174200-54212600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:54174800-54187400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:54175800-54188000	Weak transcription	Ovary	ovary
27	chr4:54176400-54186200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr4:54176400-54186200	Weak transcription	NHLF	lung
29	chr4:54176400-54187400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:54176600-54185800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:54176600-54187400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr4:54176800-54182000	Weak transcription	Psoas Muscle	Psoas
33	chr4:54179600-54181800	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr4:54179800-54187200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr4:54179800-54187200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:54180000-54181800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:54180000-54182200	Enhancers	NHDF-Ad	bronchial
38	chr4:54180000-54193200	Weak transcription	GM12878-XiMat	blood
39	chr4:54180000-54212800	Weak transcription	Primary B cells from cord blood	blood
40	chr4:54180200-54182000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:54180400-54182000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:54180400-54182000	Enhancers	Brain Substantia Nigra	brain
43	chr4:54180600-54182000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:54180600-54182400	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr4:54181000-54182000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:54181200-54181800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr4:54181200-54182000	Enhancers	Duodenum Mucosa	Duodenum
48	chr4:54181200-54182200	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr4:54181200-54182200	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr4:54181200-54182400	Enhancers	Fetal Intestine Small	intestine

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