Variant report

Variant	rs1048940
Chromosome Location	chr3:48725707-48725708
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 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	chr3:48724550-48726627	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr3:48725456-48727476	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:48724652-48725877	K562	blood:	n/a	n/a
5	POLR2A	chr3:48724095-48726734	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr3:48725528-48726668	HL-60	blood:	n/a	n/a
7	FOSL2	chr3:48725497-48726002	HepG2	liver:	n/a	n/a
8	CTCF	chr3:48725640-48725790	HCPEpiC	choroid plexus:	n/a	n/a
9	POLR2A	chr3:48725518-48726538	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:48724712-48726478	GM18505	blood:	n/a	n/a
11	POLR2A	chr3:48725299-48727383	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:48724618-48727829	HepG2	liver:	n/a	n/a
13	POLR2A	chr3:48723919-48727473	GM12891	blood:	n/a	n/a
14	POLR2A	chr3:48725506-48726554	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr3:48725492-48725919	GM12891	blood:	n/a	n/a
16	POLR2A	chr3:48723418-48727664	A549	lung:	n/a	n/a
17	POLR2A	chr3:48725602-48725910	U87	brain:	n/a	n/a
18	POLR2A	chr3:48725476-48726254	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr3:48724419-48726896	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:48725446-48727183	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr3:48722874-48727317	GM12892	blood:	n/a	n/a
22	POLR2A	chr3:48725462-48725941	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr3:48725504-48726012	K562	blood:	n/a	n/a
24	POLR2A	chr3:48723933-48726552	K562	blood:	n/a	n/a
25	POLR2A	chr3:48722064-48725822	HepG2	liver:	n/a	n/a
26	POLR2A	chr3:48724374-48726559	GM12891	blood:	n/a	n/a
27	POLR2A	chr3:48725529-48726507	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:48723060-48725786	GM12891	blood:	n/a	n/a
29	POLR2A	chr3:48725466-48725867	HepG2	liver:	n/a	n/a
30	POLR2A	chr3:48725531-48725790	MCF-7	breast:	n/a	n/a
31	POLR2A	chr3:48723842-48727720	GM12891	blood:	n/a	n/a
32	POLR2A	chr3:48725470-48726793	K562	blood:	n/a	n/a
33	POLR2A	chr3:48724727-48726615	K562	blood:	n/a	n/a
34	POLR2A	chr3:48724167-48728096	GM12892	blood:	n/a	n/a
35	POLR2A	chr3:48725456-48727325	GM12892	blood:	n/a	n/a
36	POLR2A	chr3:48724054-48727569	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:48725618-48725906	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:48725593..48727125-chr3:48750747..48752784,2	MCF-7	breast:
2	chr3:48721349..48723558-chr3:48724353..48726590,3	MCF-7	breast:
3	chr3:48725077..48727359-chr3:48728089..48729994,2	K562	blood:
4	chr3:48721678..48726571-chr3:48727447..48730865,5	K562	blood:
5	chr3:48699299..48703873-chr3:48715927..48726939,20	MCF-7	breast:
6	chr3:48725665..48728051-chr3:48734995..48736912,2	MCF-7	breast:
7	chr3:48723202..48724922-chr3:48725694..48728328,2	K562	blood:
8	chr3:48725548..48727703-chr3:48731349..48733910,3	K562	blood:

No data

Variant related genes	Relation type
NCKIPSD	TF binding region
ENSG00000008300	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000068745	Chromatin interaction
ENSG00000228350	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11706983	0.84[CEU][hapmap]
rs11708786	0.84[CEU][hapmap]
rs11709092	0.80[AMR][1000 genomes]
rs11713694	0.84[CEU][hapmap]
rs11715689	0.82[AMR][1000 genomes]
rs11715713	0.82[AMR][1000 genomes]
rs11716614	0.87[AMR][1000 genomes]
rs11719291	0.84[CEU][hapmap]
rs11719457	0.82[AMR][1000 genomes]
rs13074318	0.84[CEU][hapmap]
rs13086240	0.85[AMR][1000 genomes]
rs13090839	0.82[AMR][1000 genomes]
rs13434258	0.84[CEU][hapmap]
rs34037363	0.84[CEU][hapmap]
rs35064573	0.84[CEU][hapmap]
rs73080312	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73080361	0.87[AMR][1000 genomes]
rs9812977	0.80[AMR][1000 genomes]
rs9882549	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv590248	chr3:48716993-48727636	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1048940	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs1048940	WDR6	cis	Esophagus Mucosa	GTEx
rs1048940	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs1048940	WDR6	cis	Adipose Subcutaneous	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	chr3:48724000-48726000	Genic enhancers	Fetal Stomach	stomach
4	chr3:48724000-48727000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:48724200-48726000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:48724200-48726000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:48724200-48726400	Genic enhancers	Fetal Muscle Trunk	muscle
8	chr3:48724200-48727200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:48724200-48728400	Weak transcription	Small Intestine	intestine
10	chr3:48724200-48729600	Weak transcription	Stomach Mucosa	stomach
11	chr3:48724200-48729800	Strong transcription	Brain Germinal Matrix	brain
12	chr3:48724200-48730200	Weak transcription	K562	blood
13	chr3:48724200-48732400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:48724200-48732600	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:48724400-48729400	Strong transcription	Brain Hippocampus Middle	brain
16	chr3:48724400-48729600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:48724400-48729800	Strong transcription	HSMM	muscle
18	chr3:48724400-48730400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:48724400-48735800	Strong transcription	GM12878-XiMat	blood
20	chr3:48724600-48725800	Genic enhancers	Fetal Muscle Leg	muscle
21	chr3:48724600-48729000	Strong transcription	Esophagus	oesophagus
22	chr3:48724600-48729400	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr3:48724600-48729800	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr3:48724600-48730000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:48724600-48730000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:48724600-48730600	Strong transcription	Fetal Brain Female	brain
27	chr3:48724600-48731400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:48724600-48731800	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:48724600-48732000	Strong transcription	Fetal Lung	lung
30	chr3:48724600-48732200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:48724600-48732400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr3:48724600-48732400	Strong transcription	Fetal Intestine Large	intestine
33	chr3:48724600-48733000	Strong transcription	Primary T cells from cord blood	blood
34	chr3:48724600-48734000	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr3:48724600-48734000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:48724600-48738000	Strong transcription	Thymus	Thymus
37	chr3:48724600-48738400	Strong transcription	Primary hematopoietic stem cells	blood
38	chr3:48724600-48740400	Strong transcription	Primary B cells from cord blood	blood
39	chr3:48724600-48746600	Strong transcription	Fetal Thymus	thymus
40	chr3:48724600-48749000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:48724800-48725800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:48724800-48725800	Genic enhancers	Right Ventricle	heart
43	chr3:48724800-48726000	Genic enhancers	NHLF	lung
44	chr3:48724800-48726200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
45	chr3:48724800-48727800	Strong transcription	Pancreatic Islets	Pancreatic Islet
46	chr3:48724800-48729800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:48724800-48729800	Strong transcription	Brain Angular Gyrus	brain
48	chr3:48724800-48730000	Strong transcription	Brain Cingulate Gyrus	brain
49	chr3:48724800-48730000	Strong transcription	Brain Substantia Nigra	brain
50	chr3:48724800-48730200	Weak transcription	Right Atrium	heart

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