Variant report

Variant	rs4858830
Chromosome Location	chr3:48734002-48734003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48733764-48734149	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr3:48733924-48734138	K562	blood:	n/a	n/a
3	POLR2A	chr3:48733823-48734313	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:48733993-48734242	MCF-7	breast:	n/a	n/a
5	POLR2A	chr3:48733439-48734449	GM12892	blood:	n/a	n/a
6	POLR2A	chr3:48733879-48734026	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:48733907-48734099	H1-hESC	embryonic stem cell:	n/a	n/a
8	NR3C1	chr3:48733766-48734076	A549	lung:	n/a	chr3:48733840-48733866 chr3:48733840-48733866 chr3:48733840-48733866 chr3:48733840-48733866 chr3:48733846-48733860 chr3:48733845-48733861 chr3:48733840-48733866 chr3:48733844-48733862 chr3:48733845-48733861
9	POLR2A	chr3:48733692-48734338	A549	lung:	n/a	n/a
10	POLR2A	chr3:48733695-48734387	GM12892	blood:	n/a	n/a
11	POLR2A	chr3:48733815-48734419	GM12892	blood:	n/a	n/a
12	POLR2A	chr3:48733620-48734380	HepG2	liver:	n/a	n/a
13	POLR2A	chr3:48733873-48734390	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr3:48733740-48734399	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:48733924-48734013	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr3:48733626-48734321	GM12891	blood:	n/a	n/a
17	POLR2A	chr3:48733921-48734016	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr3:48733696-48734391	GM12891	blood:	n/a	n/a
19	POLR2A	chr3:48733835-48734431	GM12891	blood:	n/a	n/a
20	POLR2A	chr3:48733851-48734227	GM12891	blood:	n/a	n/a
21	POLR2A	chr3:48733494-48734462	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:48733826-48734056	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr3:48733983-48734002	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48699225..48701604-chr3:48731929..48734312,2	MCF-7	breast:
2	chr3:48732542..48735376-chr3:48750993..48752883,2	K562	blood:
3	chr3:48730035..48731678-chr3:48732538..48734765,2	MCF-7	breast:

Variant related genes	Relation type
IP6K2	TF binding region
ENSG00000228350	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000068745	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10865953	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12632533	1.00[CEU][hapmap]
rs14018	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4858799	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858800	1.00[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4974088	1.00[CEU][hapmap]
rs6442129	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442131	0.82[EUR][1000 genomes]
rs6766238	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6796790	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6801211	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6806356	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72929179	1.00[ASN][1000 genomes]
rs7610519	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621226	1.00[CEU][hapmap]
rs7641050	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9284885	1.00[CEU][hapmap]
rs9311431	1.00[CEU][hapmap]
rs9822485	0.92[YRI][hapmap]
rs9848268	0.95[EUR][1000 genomes]
rs9859473	1.00[CEU][hapmap]
rs9873227	0.84[EUR][1000 genomes]
rs9874010	0.92[YRI][hapmap]
rs9879978	1.00[CEU][hapmap]
rs9882443	1.00[CEU][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990211	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4858830	AMT	cis	Artery Tibial	GTEx
rs4858830	AMT	cis	lung	GTEx
rs4858830	NCKIPSD	cis	Muscle Skeletal	GTEx
rs4858830	NCKIPSD	cis	Nerve Tibial	GTEx
rs4858830	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs4858830	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs4858830	LEPR	trans	lymphoblastoid	RTeQTL
rs4858830	NICN1	cis	Thyroid	GTEx
rs4858830	AMT	cis	Adipose Subcutaneous	GTEx
rs4858830	AMT	cis	Thyroid	GTEx
rs4858830	NICN1-AS1	cis	Thyroid	GTEx
rs4858830	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs4858830	WDR6	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48724400-48735800	Strong transcription	GM12878-XiMat	blood
2	chr3:48724600-48738000	Strong transcription	Thymus	Thymus
3	chr3:48724600-48738400	Strong transcription	Primary hematopoietic stem cells	blood
4	chr3:48724600-48740400	Strong transcription	Primary B cells from cord blood	blood
5	chr3:48724600-48746600	Strong transcription	Fetal Thymus	thymus
6	chr3:48724600-48749000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:48724800-48735800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:48724800-48737600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:48724800-48738400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr3:48725000-48738600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr3:48725000-48738600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:48725000-48740400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:48725000-48740800	Strong transcription	Dnd41	blood
14	chr3:48725200-48738600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr3:48725200-48746200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:48731200-48735000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:48731400-48734400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr3:48732000-48734400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:48732000-48734400	Genic enhancers	A549	lung
20	chr3:48732200-48734400	Genic enhancers	Fetal Kidney	kidney
21	chr3:48732200-48735200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:48732400-48734400	Genic enhancers	Fetal Intestine Large	intestine
23	chr3:48732400-48736400	Genic enhancers	Primary T cells fromperipheralblood	blood
24	chr3:48732600-48734400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:48732800-48734200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:48732800-48734200	Genic enhancers	HUVEC	blood vessel
27	chr3:48732800-48734400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:48732800-48734400	Enhancers	Pancreas	Pancrea
29	chr3:48732800-48734400	Enhancers	Stomach Mucosa	stomach
30	chr3:48732800-48734400	Genic enhancers	NHEK	skin
31	chr3:48732800-48735400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr3:48732800-48744800	Weak transcription	Small Intestine	intestine
33	chr3:48732800-48745400	Weak transcription	Psoas Muscle	Psoas
34	chr3:48733000-48734200	Genic enhancers	H1 Cell Line	embryonic stem cell
35	chr3:48733000-48734200	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr3:48733000-48734200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:48733000-48734200	Enhancers	Left Ventricle	heart
38	chr3:48733000-48734400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:48733000-48734400	Enhancers	Brain Hippocampus Middle	brain
40	chr3:48733000-48734400	Enhancers	Gastric	stomach
41	chr3:48733000-48734400	Genic enhancers	NHLF	lung
42	chr3:48733000-48735600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:48733000-48736200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:48733000-48736400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:48733000-48740200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:48733000-48744800	Weak transcription	Colon Smooth Muscle	Colon
47	chr3:48733000-48745400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:48733000-48753400	Weak transcription	Aorta	Aorta
49	chr3:48733200-48734200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:48733200-48734200	Enhancers	Right Atrium	heart

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