Variant report

Variant	rs55761431
Chromosome Location	chr3:48885212-48885213
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:258)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:258 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48884487-48885528	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:48884519-48885583	A549	lung:	n/a	n/a
3	TAF1	chr3:48884932-48885297	GM12891	blood:	n/a	n/a
4	MYC	chr3:48885081-48885434	MCF-7	breast:	n/a	n/a
5	YY1	chr3:48884713-48885386	GM12878	blood:	n/a	chr3:48884749-48884763
6	POLR2A	chr3:48884470-48885782	GM12892	blood:	n/a	n/a
7	NRF1	chr3:48884979-48885562	Hela-S3	cervix:	n/a	chr3:48885321-48885332 chr3:48885358-48885369
8	TAF1	chr3:48884976-48885601	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr3:48884507-48885764	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr3:48884356-48885705	PFSK-1	brain:	n/a	n/a
11	HCFC1	chr3:48884240-48885901	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:48884885-48885634	H1-neurons	neurons:	n/a	n/a
13	RCOR1	chr3:48884463-48885506	Hela-S3	cervix:	n/a	n/a
14	YY1	chr3:48884929-48885331	H1-hESC	embryonic stem cell:	n/a	n/a
15	ELF1	chr3:48884925-48885377	K562	blood:	n/a	n/a
16	YY1	chr3:48884953-48885387	GM12891	blood:	n/a	n/a
17	MAZ	chr3:48884477-48885501	Hela-S3	cervix:	n/a	chr3:48884750-48884760
18	POLR2A	chr3:48884477-48885614	K562	blood:	n/a	n/a
19	POLR2A	chr3:48884808-48885684	GM12891	blood:	n/a	n/a
20	YY1	chr3:48885008-48885406	GM12878	blood:	n/a	n/a
21	MAX	chr3:48884335-48885665	NB4	blood:	n/a	chr3:48884750-48884760
22	HEY1	chr3:48884982-48885557	HepG2	liver:	n/a	n/a
23	CEBPB	chr3:48885170-48885550	Hela-S3	cervix:	n/a	n/a
24	NRF1	chr3:48885197-48885540	K562	blood:	n/a	chr3:48885321-48885332 chr3:48885358-48885369
25	POLR2A	chr3:48884877-48885616	GM19099	blood:	n/a	n/a
26	MAZ	chr3:48884395-48885641	GM12878	blood:	n/a	chr3:48884750-48884760
27	POLR2A	chr3:48884396-48885633	Hela-S3	cervix:	n/a	n/a
28	NR2F2	chr3:48884484-48885342	MCF-7	breast:	n/a	n/a
29	E2F6	chr3:48884388-48885439	K562	blood:	n/a	n/a
30	BCLAF1	chr3:48884803-48885285	GM12878	blood:	n/a	n/a
31	MAX	chr3:48884361-48885864	HepG2	liver:	n/a	chr3:48884750-48884760
32	POLR2A	chr3:48884894-48885752	PBDE	blood:	n/a	n/a
33	POLR2A	chr3:48884483-48885659	ECC-1	luminal epithelium:	n/a	n/a
34	RFX5	chr3:48884414-48885730	Hela-S3	cervix:	n/a	n/a
35	SMC3	chr3:48884481-48885530	Hela-S3	cervix:	n/a	n/a
36	RCOR1	chr3:48885164-48885392	HepG2	liver:	n/a	n/a
37	POLR2A	chr3:48884919-48885603	HUVEC	blood vessel:	n/a	n/a
38	MAX	chr3:48884387-48885493	GM12878	blood:	n/a	chr3:48884750-48884760
39	STAT1	chr3:48885168-48885743	GM12878	blood:	n/a	n/a
40	BHLHE40	chr3:48884300-48885635	K562	blood:	n/a	n/a
41	EBF1	chr3:48885131-48885597	GM12878	blood:	n/a	n/a
42	TAF1	chr3:48884528-48885428	HepG2	liver:	n/a	n/a
43	POLR2A	chr3:48884495-48885596	IMR90	lung:	n/a	n/a
44	TAF1	chr3:48884801-48885288	GM12878	blood:	n/a	n/a
45	HEY1	chr3:48885031-48885538	K562	blood:	n/a	n/a
46	POLR2A	chr3:48884629-48885650	GM19193	blood:	n/a	n/a
47	RUNX3	chr3:48884972-48885705	GM12878	blood:	n/a	n/a
48	ELF1	chr3:48884467-48885481	GM12878	blood:	n/a	chr3:48884751-48884763
49	POLR2A	chr3:48885111-48885554	HepG2	liver:	n/a	n/a
50	FOXA1	chr3:48885144-48885380	T-47D	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:48885189-48885239	AG10803	skin:	n/a
2	chr3:48885189-48885239	HL-60	blood:	n/a
3	chr3:48885189-48885239	HepG2	liver:	n/a
4	chr3:48885189-48885239	Jurkat	blood:	n/a
5	chr3:48885189-48885239	MCF-7	breast:	n/a
6	chr3:48885189-48885239	HCPEpiC	choroid plexus:	n/a
7	chr3:48885189-48885239	HEEpiC	esophagus:	n/a
8	chr3:48885189-48885239	GM12891	blood:	n/a
9	chr3:48885189-48885239	GM12878	blood:	n/a
10	chr3:48885189-48885239	A549	lung:	n/a
11	chr3:48885189-48885239	AG09309	skin:	n/a
12	chr3:48885189-48885239	Caco-2	colon:	n/a
13	chr3:48885189-48885239	ProgFib	skin:	n/a
14	chr3:48885189-48885239	HCF	heart:	n/a
15	chr3:48885189-48885239	SK-N-SH_RA	brain:	n/a
16	chr3:48885189-48885239	SKMC	muscle:	n/a
17	chr3:48885189-48885239	SK-N-SH	brain:	n/a
18	chr3:48885189-48885239	HPAEpiC	pulmonary alveolar:	n/a
19	chr3:48885189-48885239	RPTEC	kidney:	n/a
20	chr3:48885189-48885239	PANC-1	pancreas:	n/a
21	chr3:48885189-48885239	HRCEpiC	kidney:	n/a
22	chr3:48885189-48885239	Hepatocyte	liver:	n/a
23	chr3:48885189-48885239	ovcar-3	ovarian:	n/a
24	chr3:48885189-48885239	U87	brain:	n/a
25	chr3:48885189-48885239	PrEC	prostate:	n/a
26	chr3:48885189-48885239	AG04449	skin:	fetal
27	chr3:48885189-48885239	NHBE	bronchial:	n/a
28	chr3:48885189-48885239	AoSMC	blood vessel:	n/a
29	chr3:48885189-48885239	LNCaP	prostate:	n/a
30	chr3:48885189-48885239	HUVEC	blood vessel:	n/a
31	chr3:48885189-48885239	AG09319	gingival:	n/a
32	chr3:48885189-48885239	HCT-116	colon:	n/a
33	chr3:48885189-48885239	HIPEpiC	eye:	n/a
34	chr3:48885189-48885239	AG04450	lung:	fetal
35	chr3:48885189-48885239	CMK	blood:	n/a
36	chr3:48885189-48885239	K562	blood:	n/a
37	chr3:48885189-48885239	NB4	blood:	n/a
38	chr3:48885189-48885239	HEK293	kidney:	embryo
39	chr3:48885189-48885239	GM06990	blood:	n/a
40	chr3:48885189-48885239	Hela-S3	cervix:	n/a
41	chr3:48885189-48885239	GM12892	blood:	n/a
42	chr3:48885189-48885239	HRPEpiC	eye:	n/a
43	chr3:48885189-48885239	NT2-D1	testis:	n/a
44	chr3:48885189-48885239	HAEpiC	amniotic membrane:	n/a
45	chr3:48885189-48885239	HMEC	breast:	n/a
46	chr3:48885189-48885239	SK-N-MC	brain:	n/a
47	chr3:48885189-48885239	NH-A	brain:	n/a
48	chr3:48885189-48885239	NHDF-neo	bronchial:	n/a
49	chr3:48885189-48885239	HRE	kidney:	n/a
50	chr3:48885189-48885239	BE2_C	brain:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:193074370..193075056-chr3:48884837..48885676,2	HCT-116	colon:
2	chr3:48883728..48886453-chr3:48954781..48956546,2	MCF-7	breast:
3	chr3:48884425..48886632-chr3:49057669..49060106,3	K562	blood:
4	chr3:48882526..48887589-chr3:48952932..48958567,11	K562	blood:
5	chr12:27091126..27091875-chr3:48884781..48885512,2	Hela-S3	cervix:
6	chr3:48882526..48886164-chr3:48952991..48958735,8	K562	blood:
7	chr3:48884613..48886690-chr3:48935919..48937613,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARIH2-1	chr3:48885005-48885458	ENSG00000224424.6

No data

Variant related genes	Relation type
PRKAR2A-AS1	TF binding region
PRKAR2A-AS1	CpG island
ENSG00000178537	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000064102	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000111790	Chromatin interaction
ENSG00000177479	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000023572	Chromatin interaction
ENSG00000221883	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11708022	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11709092	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11709246	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11713694	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11715689	0.82[AMR][1000 genomes]
rs11715713	0.82[AMR][1000 genomes]
rs11715835	0.85[AMR][1000 genomes]
rs13073997	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13074318	0.85[AMR][1000 genomes]
rs13084000	0.85[AMR][1000 genomes]
rs13087930	0.85[AMR][1000 genomes]
rs13094900	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34037363	0.87[EUR][1000 genomes]
rs34477108	0.85[AMR][1000 genomes]
rs34509487	0.85[AMR][1000 genomes]
rs67060340	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67332931	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71324924	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73080361	0.88[AMR][1000 genomes];0.93[EUR][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	esv3487342	chr3:48823957-48960475	Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	esv3487343	chr3:48823963-48960381	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs55761431	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs55761431	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs55761431	WDR6	cis	Esophagus Mucosa	GTEx
rs55761431	WDR6	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48882600-48885600	Active TSS	GM12878-XiMat	blood
2	chr3:48882600-48886000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:48882800-48885600	Active TSS	NHLF	lung
4	chr3:48883000-48885800	Active TSS	Right Atrium	heart
5	chr3:48883400-48885600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:48883400-48885600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:48883400-48886000	Active TSS	Right Ventricle	heart
8	chr3:48883600-48885400	Active TSS	Hela-S3	cervix
9	chr3:48883600-48885600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:48883600-48885600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:48883600-48885800	Active TSS	NHDF-Ad	bronchial
12	chr3:48883800-48885600	Active TSS	HSMM	muscle
13	chr3:48883800-48885800	Active TSS	Ovary	ovary
14	chr3:48884000-48885400	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr3:48884000-48885400	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr3:48884000-48885400	Active TSS	NH-A	brain
17	chr3:48884000-48885600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:48884000-48885600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:48884000-48885600	Active TSS	A549	lung
20	chr3:48884000-48885800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:48884000-48885800	Active TSS	Aorta	Aorta
22	chr3:48884000-48885800	Active TSS	Psoas Muscle	Psoas
23	chr3:48884000-48886000	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr3:48884000-48886000	Active TSS	Brain Anterior Caudate	brain
25	chr3:48884000-48886200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr3:48884200-48885400	Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr3:48884200-48885400	Active TSS	Fetal Stomach	stomach
28	chr3:48884200-48885600	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr3:48884200-48885600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:48884200-48885600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:48884200-48885600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:48884200-48885600	Active TSS	Brain Angular Gyrus	brain
33	chr3:48884200-48885600	Active TSS	Brain Hippocampus Middle	brain
34	chr3:48884200-48885600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:48884200-48885600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr3:48884200-48885600	Active TSS	Fetal Intestine Large	intestine
37	chr3:48884200-48885600	Active TSS	Left Ventricle	heart
38	chr3:48884200-48885800	Active TSS	H9 Cell Line	embryonic stem cell
39	chr3:48884200-48885800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:48884200-48885800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:48884400-48885400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:48884400-48885400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:48884400-48885400	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr3:48884400-48885400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr3:48884400-48885400	Active TSS	Muscle Satellite Cultured Cells	--
46	chr3:48884400-48885400	Active TSS	Liver	Liver
47	chr3:48884400-48885400	Active TSS	Brain Cingulate Gyrus	brain
48	chr3:48884400-48885400	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr3:48884400-48885400	Active TSS	Fetal Intestine Small	intestine
50	chr3:48884400-48885400	Active TSS	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links