Variant report

Variant	rs9811027
Chromosome Location	chr3:48725014-48725015
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:51)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:51 , 50 per page) page: 1 2

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	chr3:48724852-48725345	MCF-7	breast:	n/a	n/a
4	POLR2A	chr3:48724752-48725031	HCT-116	colon:	n/a	n/a
5	POLR2A	chr3:48724548-48725051	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr3:48724652-48725877	K562	blood:	n/a	n/a
7	POLR2A	chr3:48724095-48726734	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr3:48724467-48725413	K562	blood:	n/a	n/a
9	POLR2A	chr3:48724738-48725034	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr3:48724540-48725433	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:48724920-48725220	U87	brain:	n/a	n/a
12	POLR2A	chr3:48724484-48725417	Hela-S3	cervix:	n/a	n/a
13	MTA3	chr3:48724493-48725019	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:48724538-48725056	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr3:48724712-48726478	GM18505	blood:	n/a	n/a
16	POLR2A	chr3:48724237-48725444	HepG2	liver:	n/a	n/a
17	USF2	chr3:48725003-48725398	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr3:48724540-48725386	GM12891	blood:	n/a	n/a
19	POLR2A	chr3:48724427-48725441	GM12892	blood:	n/a	n/a
20	POLR2A	chr3:48724537-48725421	K562	blood:	n/a	n/a
21	POLR2A	chr3:48724618-48727829	HepG2	liver:	n/a	n/a
22	POLR2A	chr3:48723919-48727473	GM12891	blood:	n/a	n/a
23	POLR2A	chr3:48724496-48725353	HCT-116	colon:	n/a	n/a
24	POLR2A	chr3:48722946-48725300	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr3:48723418-48727664	A549	lung:	n/a	n/a
26	POLR2A	chr3:48724539-48725339	GM12878	blood:	n/a	n/a
27	POLR2A	chr3:48724419-48726896	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:48722874-48727317	GM12892	blood:	n/a	n/a
29	POLR2A	chr3:48722860-48725381	SK-N-MC	brain:	n/a	n/a
30	POLR2A	chr3:48724610-48725083	HepG2	liver:	n/a	n/a
31	POLR2A	chr3:48723933-48726552	K562	blood:	n/a	n/a
32	POLR2A	chr3:48724749-48725446	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr3:48724551-48725274	HepG2	liver:	n/a	n/a
34	POLR2A	chr3:48722064-48725822	HepG2	liver:	n/a	n/a
35	POLR2A	chr3:48724374-48726559	GM12891	blood:	n/a	n/a
36	POLR2A	chr3:48723014-48725451	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr3:48724545-48725448	HL-60	blood:	n/a	n/a
38	POLR2A	chr3:48723060-48725786	GM12891	blood:	n/a	n/a
39	POLR2A	chr3:48724617-48725440	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr3:48724457-48725408	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr3:48724460-48725220	U87	brain:	n/a	n/a
42	POLR2A	chr3:48723842-48727720	GM12891	blood:	n/a	n/a
43	POLR2A	chr3:48722893-48725354	U87	brain:	n/a	n/a
44	POLR2A	chr3:48724526-48725422	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr3:48724727-48726615	K562	blood:	n/a	n/a
46	POLR2A	chr3:48724167-48728096	GM12892	blood:	n/a	n/a
47	FOSL2	chr3:48724314-48725396	HepG2	liver:	n/a	n/a
48	POLR2A	chr3:48724226-48725350	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr3:48722887-48725354	U87	brain:	n/a	n/a
50	POLR2A	chr3:48724408-48725203	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:48646668..48648790-chr3:48722957..48725638,2	K562	blood:
2	chr3:48721349..48723558-chr3:48724353..48726590,3	MCF-7	breast:
3	chr3:48721678..48726571-chr3:48727447..48730865,5	K562	blood:
4	chr3:48699299..48703873-chr3:48715927..48726939,20	MCF-7	breast:
5	chr3:48596333..48598381-chr3:48723382..48725322,2	K562	blood:
6	chr3:48720678..48725638-chr3:48726169..48732697,10	MCF-7	breast:

No data

Variant related genes	Relation type
NCKIPSD	TF binding region
ENSG00000068745	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000010256	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000114268	Chromatin interaction
ENSG00000008300	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10865952	0.95[ASN][1000 genomes]
rs11557629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11706203	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713694	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs11715177	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715689	0.80[AMR][1000 genomes]
rs11715713	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11715835	0.81[ASN][1000 genomes]
rs11719291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719457	0.80[AMR][1000 genomes]
rs11928552	1.00[JPT][hapmap]
rs12107418	0.81[EUR][1000 genomes]
rs12493289	1.00[JPT][hapmap]
rs12493578	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12497850	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12715429	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13063223	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070798	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13074318	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs13076269	0.81[AMR][1000 genomes]
rs13086240	0.84[AMR][1000 genomes]
rs13090013	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090839	0.80[AMR][1000 genomes]
rs13096357	0.81[AMR][1000 genomes]
rs13316551	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324119	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13324950	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352420	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17080319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286651	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2286652	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2302295	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28452701	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28567949	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28657585	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28793701	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34037363	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs34096717	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34153629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34577723	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35064573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733086	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3806694	1.00[JPT][hapmap]
rs3821875	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4077495	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858798	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4858828	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4858831	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs56735597	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61137521	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6442130	1.00[CHB][hapmap]
rs6768448	0.85[EUR][1000 genomes]
rs6773261	0.81[AMR][1000 genomes]
rs6788650	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs68042649	0.85[EUR][1000 genomes]
rs73078362	0.81[EUR][1000 genomes]
rs7428949	1.00[JPT][hapmap]
rs7627404	1.00[CHB][hapmap]
rs7633840	0.86[ASN][1000 genomes]
rs9809222	0.85[EUR][1000 genomes]
rs9811318	0.85[EUR][1000 genomes]
rs9812200	0.83[EUR][1000 genomes]
rs9812977	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9821797	0.85[EUR][1000 genomes]
rs9834996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835307	1.00[CHB][hapmap]
rs9836462	0.85[EUR][1000 genomes]
rs9841602	0.85[EUR][1000 genomes]
rs9848203	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9854034	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9873726	1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs9877542	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877685	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9811027	WDR6	cis	Esophagus Mucosa	GTEx
rs9811027	WDR6	cis	Whole Blood	GTEx
rs9811027	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9811027	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs9811027	WDR6	cis	Adipose Subcutaneous	GTEx
rs9811027	WDR6	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48718800-48725600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:48723800-48725400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:48723800-48725400	Enhancers	Fetal Heart	heart
4	chr3:48723800-48725600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:48723800-48732200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:48723800-48733800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:48724000-48725200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:48724000-48725200	Weak transcription	Fetal Brain Male	brain
9	chr3:48724000-48726000	Genic enhancers	Fetal Stomach	stomach
10	chr3:48724000-48727000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:48724200-48725200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:48724200-48725200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr3:48724200-48726000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr3:48724200-48726000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr3:48724200-48726400	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr3:48724200-48727200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:48724200-48728400	Weak transcription	Small Intestine	intestine
18	chr3:48724200-48729600	Weak transcription	Stomach Mucosa	stomach
19	chr3:48724200-48729800	Strong transcription	Brain Germinal Matrix	brain
20	chr3:48724200-48730200	Weak transcription	K562	blood
21	chr3:48724200-48732400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:48724200-48732600	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:48724400-48725200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:48724400-48725200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr3:48724400-48725200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr3:48724400-48725200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:48724400-48725200	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:48724400-48725200	Enhancers	Psoas Muscle	Psoas
29	chr3:48724400-48729400	Strong transcription	Brain Hippocampus Middle	brain
30	chr3:48724400-48729600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:48724400-48729800	Strong transcription	HSMM	muscle
32	chr3:48724400-48730400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:48724400-48735800	Strong transcription	GM12878-XiMat	blood
34	chr3:48724600-48725200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:48724600-48725200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr3:48724600-48725200	Genic enhancers	NHEK	skin
37	chr3:48724600-48725400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:48724600-48725400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:48724600-48725400	Genic enhancers	Rectal Smooth Muscle	rectum
40	chr3:48724600-48725400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
41	chr3:48724600-48725400	Genic enhancers	Stomach Smooth Muscle	stomach
42	chr3:48724600-48725800	Genic enhancers	Fetal Muscle Leg	muscle
43	chr3:48724600-48729000	Strong transcription	Esophagus	oesophagus
44	chr3:48724600-48729400	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr3:48724600-48729800	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr3:48724600-48730000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:48724600-48730000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:48724600-48730600	Strong transcription	Fetal Brain Female	brain
49	chr3:48724600-48731400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:48724600-48731800	Strong transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links