Variant report

Variant	rs4858799
Chromosome Location	chr3:48728204-48728205
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48723848-48729026	GM12892	blood:	n/a	n/a
2	POLR2A	chr3:48727621-48728944	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:48728124-48728728	GM12892	blood:	n/a	n/a
4	POLR2A	chr3:48727624-48728724	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:48728184-48728858	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:48728065-48728304	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48708844..48711305-chr3:48727090..48731325,3	K562	blood:
2	chr3:48720678..48725638-chr3:48726169..48732697,10	MCF-7	breast:
3	chr3:48725077..48727359-chr3:48728089..48729994,2	K562	blood:
4	chr3:48727679..48729192-chr3:48743162..48745800,2	K562	blood:
5	chr3:48646300..48647842-chr3:48725796..48728782,2	K562	blood:
6	chr3:48721678..48726571-chr3:48727447..48730865,5	K562	blood:
7	chr3:48725798..48728623-chr3:48730156..48733181,3	K562	blood:
8	chr3:48723202..48724922-chr3:48725694..48728328,2	K562	blood:

No data

Variant related genes	Relation type
NCKIPSD	TF binding region
ENSG00000271973	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000068745	Chromatin interaction
ENSG00000010256	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10865953	0.98[EUR][1000 genomes]
rs14018	0.81[EUR][1000 genomes]
rs4858800	0.98[EUR][1000 genomes]
rs4858830	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442129	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442131	0.82[EUR][1000 genomes]
rs6766238	0.83[EUR][1000 genomes]
rs6796790	0.84[EUR][1000 genomes]
rs6801211	0.84[EUR][1000 genomes]
rs6806356	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7610519	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7641050	0.96[EUR][1000 genomes]
rs9848268	0.95[EUR][1000 genomes]
rs9873227	0.84[EUR][1000 genomes]
rs9882443	0.96[EUR][1000 genomes]
rs990211	0.82[AMR][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	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4858799	AMT	cis	Thyroid	GTEx
rs4858799	NCKIPSD	cis	Muscle Skeletal	GTEx
rs4858799	AMT	cis	Artery Tibial	GTEx
rs4858799	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs4858799	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs4858799	NICN1	cis	Thyroid	GTEx
rs4858799	NICN1-AS1	cis	Thyroid	GTEx
rs4858799	WDR6	cis	Muscle Skeletal	GTEx
rs4858799	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs4858799	NCKIPSD	cis	Nerve Tibial	GTEx
rs4858799	AMT	cis	lung	GTEx
rs4858799	AMT	cis	Artery Aorta	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48723800-48732200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:48723800-48733800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:48724200-48728400	Weak transcription	Small Intestine	intestine
4	chr3:48724200-48729600	Weak transcription	Stomach Mucosa	stomach
5	chr3:48724200-48729800	Strong transcription	Brain Germinal Matrix	brain
6	chr3:48724200-48730200	Weak transcription	K562	blood
7	chr3:48724200-48732400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:48724200-48732600	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:48724400-48729400	Strong transcription	Brain Hippocampus Middle	brain
10	chr3:48724400-48729600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:48724400-48729800	Strong transcription	HSMM	muscle
12	chr3:48724400-48730400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:48724400-48735800	Strong transcription	GM12878-XiMat	blood
14	chr3:48724600-48729000	Strong transcription	Esophagus	oesophagus
15	chr3:48724600-48729400	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr3:48724600-48729800	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr3:48724600-48730000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:48724600-48730000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:48724600-48730600	Strong transcription	Fetal Brain Female	brain
20	chr3:48724600-48731400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:48724600-48731800	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:48724600-48732000	Strong transcription	Fetal Lung	lung
23	chr3:48724600-48732200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:48724600-48732400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:48724600-48732400	Strong transcription	Fetal Intestine Large	intestine
26	chr3:48724600-48733000	Strong transcription	Primary T cells from cord blood	blood
27	chr3:48724600-48734000	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:48724600-48734000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:48724600-48738000	Strong transcription	Thymus	Thymus
30	chr3:48724600-48738400	Strong transcription	Primary hematopoietic stem cells	blood
31	chr3:48724600-48740400	Strong transcription	Primary B cells from cord blood	blood
32	chr3:48724600-48746600	Strong transcription	Fetal Thymus	thymus
33	chr3:48724600-48749000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:48724800-48729800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:48724800-48729800	Strong transcription	Brain Angular Gyrus	brain
36	chr3:48724800-48730000	Strong transcription	Brain Cingulate Gyrus	brain
37	chr3:48724800-48730000	Strong transcription	Brain Substantia Nigra	brain
38	chr3:48724800-48730200	Weak transcription	Right Atrium	heart
39	chr3:48724800-48730200	Strong transcription	HSMMtube	muscle
40	chr3:48724800-48730800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:48724800-48731000	Strong transcription	Adipose Nuclei	Adipose
42	chr3:48724800-48731200	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:48724800-48731200	Strong transcription	Fetal Kidney	kidney
44	chr3:48724800-48731200	Strong transcription	HUVEC	blood vessel
45	chr3:48724800-48731400	Strong transcription	Aorta	Aorta
46	chr3:48724800-48731600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:48724800-48731600	Strong transcription	Hela-S3	cervix
48	chr3:48724800-48732000	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr3:48724800-48732200	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr3:48724800-48732200	Strong transcription	Pancreas	Pancrea

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