Variant report

Variant	rs4858795
Chromosome Location	chr3:48515079-48515080
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	chr3:48513742-48515182	GM12892	blood:	n/a	n/a
2	SP1	chr3:48514268-48515267	HepG2	liver:	n/a	chr3:48514641-48514655 chr3:48514608-48514620 chr3:48514610-48514619 chr3:48514608-48514620 chr3:48514608-48514619 chr3:48514659-48514670 chr3:48514644-48514656 chr3:48514645-48514654 chr3:48514644-48514655 chr3:48514816-48514825 chr3:48514815-48514825 chr3:48514646-48514655 chr3:48514644-48514656 chr3:48514609-48514618
3	FOXA1	chr3:48514473-48515099	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:48514193-48515257	HepG2	liver:	n/a	n/a
5	CTBP2	chr3:48514472-48515094	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr3:48514034-48515176	A549	lung:	n/a	chr3:48514749-48514770 chr3:48514750-48514759
7	MAX	chr3:48513900-48515275	A549	lung:	n/a	n/a
8	CREB1	chr3:48514088-48515385	HepG2	liver:	n/a	chr3:48514543-48514556
9	MAZ	chr3:48514159-48515130	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:48513747-48515186	Hela-S3	cervix:	n/a	n/a
11	HNF4A	chr3:48514487-48515229	HepG2	liver:	n/a	chr3:48514930-48514945
12	SMC3	chr3:48514678-48515112	HepG2	liver:	n/a	n/a
13	MAX	chr3:48513590-48515117	K562	blood:	n/a	n/a
14	REST	chr3:48513768-48515236	H1-neurons	neurons:	n/a	chr3:48514809-48514822 chr3:48514610-48514623 chr3:48514617-48514627
15	MYBL2	chr3:48514277-48515268	HepG2	liver:	n/a	n/a
16	POLR2A	chr3:48514153-48515184	HepG2	liver:	n/a	n/a
17	MYC	chr3:48514102-48515115	K562	blood:	n/a	n/a
18	POLR2A	chr3:48514098-48515082	HCT-116	colon:	n/a	n/a
19	HDAC2	chr3:48514300-48515172	HepG2	liver:	n/a	n/a
20	ELF1	chr3:48514195-48515082	HepG2	liver:	n/a	chr3:48514649-48514661
21	MYC	chr3:48514311-48515158	HepG2	liver:	n/a	n/a
22	CEBPB	chr3:48514755-48515161	HepG2	liver:	n/a	n/a
23	YY1	chr3:48514076-48515091	HepG2	liver:	n/a	chr3:48514596-48514615 chr3:48514652-48514663
24	YY1	chr3:48513924-48515106	GM12878	blood:	n/a	chr3:48514596-48514615 chr3:48514652-48514663
25	NFIC	chr3:48514452-48515221	HepG2	liver:	n/a	chr3:48514623-48514639
26	ATF2	chr3:48514119-48515195	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAFK	chr3:48514692-48515248	HepG2	liver:	n/a	chr3:48514821-48514836
28	CTCF	chr3:48515020-48515170	Hela-S3	cervix:	n/a	n/a
29	MAX	chr3:48513794-48515207	NB4	blood:	n/a	n/a
30	MAX	chr3:48514018-48515397	HepG2	liver:	n/a	n/a
31	MAX	chr3:48514225-48515156	HepG2	liver:	n/a	n/a
32	POLR2A	chr3:48513744-48515134	H1-hESC	embryonic stem cell:	n/a	n/a
33	JUND	chr3:48514354-48515092	HepG2	liver:	n/a	chr3:48514545-48514554
34	MYC	chr3:48514079-48515335	A549	lung:	n/a	n/a
35	YY1	chr3:48514005-48515088	GM12892	blood:	n/a	chr3:48514596-48514615 chr3:48514652-48514663
36	POLR2A	chr3:48514020-48515167	H1-hESC	embryonic stem cell:	n/a	n/a
37	MTA3	chr3:48513926-48515117	GM12878	blood:	n/a	n/a
38	MAX	chr3:48514100-48515261	A549	lung:	n/a	n/a
39	SP1	chr3:48514198-48515119	H1-hESC	embryonic stem cell:	n/a	chr3:48514641-48514655 chr3:48514608-48514620 chr3:48514610-48514619 chr3:48514608-48514620 chr3:48514608-48514619 chr3:48514659-48514670 chr3:48514644-48514656 chr3:48514645-48514654 chr3:48514644-48514655 chr3:48514816-48514825 chr3:48514815-48514825 chr3:48514646-48514655 chr3:48514644-48514656 chr3:48514609-48514618
40	MYBL2	chr3:48514093-48515207	HepG2	liver:	n/a	n/a
41	EP300	chr3:48514348-48515239	HepG2	liver:	n/a	chr3:48514610-48514626 chr3:48514649-48514658
42	REST	chr3:48514599-48515148	HepG2	liver:	n/a	chr3:48514809-48514822 chr3:48514610-48514623 chr3:48514617-48514627
43	HEY1	chr3:48514100-48515168	HepG2	liver:	n/a	chr3:48514646-48514661 chr3:48514546-48514555 chr3:48514544-48514553
44	POLR2A	chr3:48513825-48515287	U87	brain:	n/a	n/a
45	FOSL2	chr3:48514293-48515154	HepG2	liver:	n/a	chr3:48514545-48514554
46	CTCF	chr3:48515000-48515150	AG04450	lung:	n/a	n/a
47	ELF1	chr3:48513977-48515083	GM12878	blood:	n/a	chr3:48514649-48514661
48	MXI1	chr3:48514193-48515163	HepG2	liver:	n/a	n/a
49	MAX	chr3:48514073-48515112	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr3:48513420-48515229	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48512815..48516100-chr3:48594601..48597600,3	K562	blood:
2	chr3:48506857..48510517-chr3:48512823..48515674,4	MCF-7	breast:
3	chr3:48512987..48515121-chr3:48538907..48542764,4	MCF-7	breast:
4	chr3:48514107..48516088-chr3:48667675..48669788,2	K562	blood:
5	chr3:48505885..48511674-chr3:48512501..48516993,10	K562	blood:
6	chr3:48281039..48283392-chr3:48513120..48515828,2	K562	blood:
7	chr3:48511787..48515469-chr3:48539737..48543035,4	K562	blood:
8	chr3:48481215..48483251-chr3:48514789..48517662,2	K562	blood:
9	chr3:48513069..48515559-chr3:48519678..48521467,2	K562	blood:
10	chr3:48515040..48517957-chr3:48545083..48546816,2	MCF-7	breast:
11	chr3:48504031..48516338-chr3:48532689..48546353,31	MCF-7	breast:
12	chr3:48515011..48517964-chr3:48519270..48521747,2	MCF-7	breast:
13	chr3:48514328..48516205-chr3:48592157..48594449,2	K562	blood:

Variant related genes	Relation type
SHISA5	TF binding region
ENSG00000164051	Chromatin interaction
ENSG00000213689	Chromatin interaction
ENSG00000114268	Chromatin interaction
ENSG00000164048	Chromatin interaction
ENSG00000232112	Chromatin interaction
ENSG00000164054	Chromatin interaction
ENSG00000225697	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1037773	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs10470686	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs1109227	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs11130170	0.90[JPT][hapmap]
rs11130171	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs11797	0.84[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs13072012	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs13076076	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs13314659	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs1459242	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs1563736	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs1870444	0.80[AMR][1000 genomes]
rs2045554	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2242150	0.84[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2279077	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs2290822	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs2362450	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs2362452	0.82[CHD][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.95[YRI][hapmap]
rs2885510	0.94[JPT][hapmap]
rs3214041	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs3774808	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs4858819	0.85[JPT][hapmap]
rs6442117	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs6442118	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs6442119	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs6442120	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs6764415	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6776700	0.84[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs6794875	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs725309	0.89[JPT][hapmap]
rs725310	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs730566	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs734071	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs734072	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7636044	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs7651407	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs898225	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs922075	0.88[ASW][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9311428	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9812647	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs9815088	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9815103	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs9838618	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs9849509	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs9876781	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs9883759	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs9883927	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv1802114	chr3:48498822-48577670	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv590243	chr3:48505831-48519821	Flanking Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv590244	chr3:48505924-48519821	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv590245	chr3:48506222-48519821	Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4858795	RP11-24C3.2	cis	Muscle Skeletal	GTEx
rs4858795	AMT	cis	parietal	SCAN
rs4858795	ALAS1	cis	parietal	SCAN
rs4858795	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs4858795	GMPPB	cis	parietal	SCAN
rs4858795	TMA7	cis	Muscle Skeletal	GTEx
rs4858795	ZNF589	cis	parietal	SCAN
rs4858795	SHISA5	cis	lymphoblastoid	seeQTL
rs4858795	C3orf18	cis	cerebellum	SCAN
rs4858795	NICN1	cis	cerebellum	SCAN
rs4858795	ATRIP	cis	Cerebellum	GTEx
rs4858795	CXCR6	cis	parietal	SCAN
rs4858795	TMEM158	cis	parietal	SCAN
rs4858795	AMT	cis	cerebellum	SCAN
rs4858795	PLXNB1	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48513200-48515200	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr3:48513400-48515200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:48513400-48515200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
4	chr3:48513400-48515200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr3:48514000-48515200	Flanking Active TSS	GM12878-XiMat	blood
6	chr3:48514400-48515200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:48514600-48515200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:48514600-48515200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:48514600-48515200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:48514600-48515200	Enhancers	Primary B cells from cord blood	blood
11	chr3:48514600-48515200	Enhancers	Primary hematopoietic stem cells	blood
12	chr3:48514600-48515200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:48514600-48515200	Flanking Active TSS	Liver	Liver
14	chr3:48514600-48515200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
15	chr3:48514600-48515200	Enhancers	Fetal Brain Male	brain
16	chr3:48514600-48515200	Flanking Active TSS	Fetal Thymus	thymus
17	chr3:48514600-48515200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
18	chr3:48514600-48515200	Enhancers	Small Intestine	intestine
19	chr3:48514600-48515200	Flanking Active TSS	Stomach Mucosa	stomach
20	chr3:48514600-48515200	Enhancers	HUVEC	blood vessel
21	chr3:48514600-48515400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:48514600-48515400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:48514600-48515400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr3:48514600-48515400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr3:48514600-48515400	Enhancers	Placenta Amnion	Placenta Amnion
26	chr3:48514600-48515600	Enhancers	H1 Cell Line	embryonic stem cell
27	chr3:48514600-48515600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:48514600-48515600	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr3:48514600-48516800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr3:48514600-48535600	Weak transcription	Ovary	ovary
31	chr3:48514800-48515200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:48514800-48515200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:48514800-48515200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr3:48514800-48515200	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr3:48514800-48515200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr3:48514800-48515200	Flanking Active TSS	Brain Hippocampus Middle	brain
37	chr3:48514800-48515200	Enhancers	Lung	lung
38	chr3:48514800-48515200	Flanking Active TSS	A549	lung
39	chr3:48514800-48515200	Flanking Active TSS	Hela-S3	cervix
40	chr3:48514800-48515200	Flanking Active TSS	K562	blood
41	chr3:48514800-48515200	Enhancers	NHEK	skin
42	chr3:48514800-48515600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:48514800-48516400	Enhancers	Placenta	Placenta
44	chr3:48514800-48541000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr3:48515000-48515200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr3:48515000-48515200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:48515000-48515200	Enhancers	H9 Cell Line	embryonic stem cell
48	chr3:48515000-48515200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:48515000-48515200	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr3:48515000-48515200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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