Variant report

Variant	rs4858094
Chromosome Location	chr3:23918616-23918617
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23916969..23919242-chr3:23920900..23922726,2	K562	blood:
2	chr3:23910955..23912484-chr3:23917775..23920072,2	MCF-7	breast:
3	chr3:23850691..23852866-chr3:23917771..23919785,2	MCF-7	breast:
4	chr3:23916300..23920243-chr3:23955913..23960326,5	K562	blood:
5	chr3:23913990..23915626-chr3:23916378..23919022,2	K562	blood:
6	chr3:23916456..23919373-chr3:23958653..23961200,2	MCF-7	breast:
7	chr3:23908978..23911720-chr3:23917649..23919406,2	K562	blood:

Variant related genes	Relation type
ENSG00000174748	Chromatin interaction
ENSG00000231395	Chromatin interaction
ENSG00000197885	Chromatin interaction
ENSG00000170142	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1026407	0.90[JPT][hapmap]
rs11707828	1.00[JPT][hapmap]
rs11717862	0.82[EUR][1000 genomes]
rs12631785	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13091509	0.86[EUR][1000 genomes]
rs13095392	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs1471060	1.00[JPT][hapmap]
rs1473380	0.86[JPT][hapmap];0.83[MEX][hapmap]
rs1473381	0.86[JPT][hapmap]
rs4024642	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4025822	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4131403	0.83[EUR][1000 genomes]
rs4241514	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4241517	0.96[CEU][hapmap];0.96[GIH][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs4241520	0.81[EUR][1000 genomes]
rs4321479	0.92[CEU][hapmap];0.88[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs4546101	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4589882	0.92[CEU][hapmap];0.88[GIH][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs4619734	0.82[EUR][1000 genomes]
rs4858095	0.91[CEU][hapmap];0.88[GIH][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs4858098	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4858548	0.80[ASN][1000 genomes]
rs4858549	0.81[ASN][1000 genomes]
rs4858550	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4858551	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858553	0.91[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858567	0.92[CEU][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs4858569	0.84[MEX][hapmap];0.83[TSI][hapmap]
rs5023610	0.92[CEU][hapmap]
rs6550804	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6550807	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6550815	0.89[EUR][1000 genomes]
rs6550819	0.85[EUR][1000 genomes]
rs6550823	0.92[CEU][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs6762238	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6764154	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779476	0.87[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs6790557	0.81[EUR][1000 genomes]
rs6794922	0.92[CEU][hapmap];0.88[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs6807856	0.91[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs7371944	0.87[CEU][hapmap];0.80[GIH][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs7431301	0.81[EUR][1000 genomes]
rs7615009	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7615255	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7626431	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7627709	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7636810	0.88[TSI][hapmap]
rs7648931	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7651185	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9842907	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9845287	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9863320	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9869299	0.91[JPT][hapmap]
rs9882735	0.80[EUR][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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4858094	C3orf48	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23901200-23942000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:23901800-23928800	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr3:23901800-23935600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:23903400-23929400	Weak transcription	Dnd41	blood
5	chr3:23904800-23930800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:23906400-23922000	Weak transcription	Primary T cells from cord blood	blood
7	chr3:23906600-23931800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:23907000-23920400	Weak transcription	Primary B cells from cord blood	blood
9	chr3:23907600-23920000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:23907600-23922200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr3:23907600-23940200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:23908000-23918800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:23908000-23922400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr3:23908000-23923600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:23908000-23931600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr3:23908000-23935600	Weak transcription	Fetal Kidney	kidney
17	chr3:23908000-23935600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:23908000-23940200	Weak transcription	Gastric	stomach
19	chr3:23908200-23919400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:23908200-23930400	Weak transcription	HepG2	liver
21	chr3:23911800-23922600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:23912000-23919000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:23912000-23919800	Weak transcription	Fetal Stomach	stomach
24	chr3:23912000-23923400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:23912200-23918800	Weak transcription	Fetal Thymus	thymus
26	chr3:23912200-23919800	Weak transcription	Fetal Intestine Small	intestine
27	chr3:23912200-23922000	Weak transcription	K562	blood
28	chr3:23912200-23930200	Weak transcription	Liver	Liver
29	chr3:23914000-23924000	Weak transcription	Fetal Intestine Large	intestine
30	chr3:23914600-23919600	Enhancers	NHDF-Ad	bronchial
31	chr3:23914800-23919800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr3:23915200-23919800	Enhancers	Fetal Heart	heart
33	chr3:23915200-23919800	Enhancers	NHLF	lung
34	chr3:23915400-23918800	Weak transcription	Small Intestine	intestine
35	chr3:23915400-23919400	Enhancers	Brain Hippocampus Middle	brain
36	chr3:23915400-23919600	Enhancers	HUVEC	blood vessel
37	chr3:23915800-23921000	Strong transcription	GM12878-XiMat	blood
38	chr3:23915800-23923200	Weak transcription	Esophagus	oesophagus
39	chr3:23916000-23923400	Weak transcription	Fetal Brain Female	brain
40	chr3:23916000-23934000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr3:23916000-23950200	Weak transcription	Aorta	Aorta
42	chr3:23916200-23921000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr3:23916200-23948800	Weak transcription	Colonic Mucosa	Colon
44	chr3:23916600-23932800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr3:23916800-23922200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr3:23917000-23919400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr3:23917200-23919600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:23917200-23931600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr3:23917600-23919600	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr3:23917600-23920000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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