Variant report

Variant	rs3809547
Chromosome Location	chr15:75628841-75628842
allele	C/G
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	chr15:75628074-75629348	K562	blood:	n/a	n/a
2	POLR2A	chr15:75627992-75628872	Hela-S3	cervix:	n/a	n/a
3	SIX5	chr15:75627612-75628991	A549	lung:	n/a	chr15:75627639-75627648
4	POLR2A	chr15:75627976-75629400	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr15:75628840-75629057	HUVEC	blood vessel:	n/a	n/a
6	CHD1	chr15:75628820-75628843	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr15:75628065-75628871	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr15:75627977-75629397	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr15:75628070-75629387	K562	blood:	n/a	n/a
10	ELF1	chr15:75628170-75628847	GM12878	blood:	n/a	n/a
11	POLR2A	chr15:75627584-75628875	PFSK-1	brain:	n/a	n/a
12	REST	chr15:75628021-75628877	H1-neurons	neurons:	n/a	chr15:75628303-75628313 chr15:75628246-75628259
13	MYBL2	chr15:75627935-75628905	HepG2	liver:	n/a	n/a
14	POLR2A	chr15:75628251-75628846	IMR90	lung:	n/a	n/a
15	MXI1	chr15:75627573-75629389	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr15:75627819-75629400	H1-hESC	embryonic stem cell:	n/a	n/a
17	E2F4	chr15:75628084-75628842	Hela-S3	cervix:	n/a	chr15:75628323-75628333 chr15:75628590-75628602 chr15:75628608-75628617
18	POLR2A	chr15:75627925-75629338	PANC-1	pancreas:	n/a	n/a
19	POLR2A	chr15:75627999-75629119	PBDE	blood:	n/a	n/a
20	MAX	chr15:75627883-75628843	A549	lung:	n/a	chr15:75628355-75628368 chr15:75628358-75628367 chr15:75628327-75628337 chr15:75628357-75628366 chr15:75628355-75628368 chr15:75628355-75628363 chr15:75628687-75628697 chr15:75628357-75628366 chr15:75628355-75628368 chr15:75628356-75628367
21	HEY1	chr15:75628020-75629287	K562	blood:	n/a	n/a
22	REST	chr15:75627887-75629131	A549	lung:	n/a	chr15:75628303-75628313 chr15:75628246-75628259
23	USF1	chr15:75628013-75628867	A549	lung:	n/a	chr15:75628048-75628064 chr15:75628355-75628368 chr15:75628357-75628366 chr15:75628356-75628365 chr15:75628351-75628372 chr15:75628357-75628366
24	USF1	chr15:75627982-75628853	HCT-116	colon:	n/a	chr15:75628048-75628064 chr15:75628355-75628368 chr15:75628357-75628366 chr15:75628356-75628365 chr15:75628351-75628372 chr15:75628357-75628366
25	POLR2A	chr15:75628044-75629006	Hela-S3	cervix:	n/a	n/a
26	TAF1	chr15:75627973-75628885	A549	lung:	n/a	n/a
27	MAZ	chr15:75627993-75629004	IMR90	lung:	n/a	chr15:75628355-75628368 chr15:75628358-75628367 chr15:75628327-75628337 chr15:75628357-75628366 chr15:75628355-75628368 chr15:75628355-75628363 chr15:75628687-75628697 chr15:75628357-75628366 chr15:75628355-75628368 chr15:75628356-75628367
28	SIN3AK20	chr15:75628054-75628890	MCF-7	breast:	n/a	n/a
29	HCFC1	chr15:75627403-75629468	Hela-S3	cervix:	n/a	n/a
30	TCF12	chr15:75627741-75628999	A549	lung:	n/a	n/a
31	SIN3AK20	chr15:75627953-75628878	MCF-7	breast:	n/a	n/a
32	POLR2A	chr15:75627792-75629615	SK-N-MC	brain:	n/a	n/a
33	MTA3	chr15:75628068-75629043	GM12878	blood:	n/a	n/a
34	POLR2A	chr15:75627734-75629554	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75626715..75630609-chr15:75659083..75662163,7	K562	blood:
2	chr15:75626956..75629637-chr15:75642872..75644867,2	MCF-7	breast:
3	chr15:75626774..75630064-chr15:75654261..75656966,3	K562	blood:
4	chr15:75626851..75629633-chr15:75646566..75649228,2	K562	blood:
5	chr15:75628015..75635137-chr15:75659177..75662618,8	MCF-7	breast:
6	chr15:75628778..75631510-chr15:75648708..75650958,2	MCF-7	breast:
7	chr15:75626494..75629832-chr15:75639090..75642248,3	MCF-7	breast:
8	chr15:75627175..75629335-chr15:75660124..75661831,2	MCF-7	breast:
9	chr15:75627797..75629612-chr15:75743113..75745396,2	K562	blood:
10	chr15:75246342..75249068-chr15:75626976..75630362,3	K562	blood:
11	chr15:75628335..75630040-chr15:75940132..75942573,2	MCF-7	breast:
12	chr15:75493870..75496515-chr15:75627756..75630428,2	K562	blood:

Variant related genes	Relation type
COMMD4	TF binding region
ENSG00000140398	Chromatin interaction
ENSG00000140400	Chromatin interaction
ENSG00000178718	Chromatin interaction
ENSG00000169375	Chromatin interaction
ENSG00000167173	Chromatin interaction
ENSG00000177971	Chromatin interaction
ENSG00000260591	Chromatin interaction
ENSG00000173548	Chromatin interaction
ENSG00000260274	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10152155	0.88[EUR][1000 genomes]
rs10220738	0.94[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10775209	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11072542	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11631052	0.89[EUR][1000 genomes]
rs11634863	0.83[EUR][1000 genomes]
rs11636031	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs11636199	0.94[CEU][hapmap]
rs11637068	0.89[EUR][1000 genomes]
rs11638974	0.94[CEU][hapmap]
rs12708519	0.94[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs28610581	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs28737338	0.80[EUR][1000 genomes]
rs4243033	0.88[EUR][1000 genomes]
rs4297648	0.86[EUR][1000 genomes]
rs4299117	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs4322627	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs4368141	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4451914	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs4462560	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4486847	0.87[EUR][1000 genomes]
rs4545784	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs4564532	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886443	0.94[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886446	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs4886699	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4886700	0.88[EUR][1000 genomes]
rs4886703	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs4886707	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs4886708	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs5745920	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6495171	0.91[JPT][hapmap]
rs6495182	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs7166737	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7171507	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7175852	0.88[EUR][1000 genomes]
rs7180574	0.80[EUR][1000 genomes]
rs7402293	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7402844	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8023268	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs8023815	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs8024244	0.80[EUR][1000 genomes]
rs8028277	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8029112	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs8029394	0.89[EUR][1000 genomes]
rs8030802	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs8034317	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs8036758	0.80[EUR][1000 genomes]
rs8038760	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039713	chr15:75394213-75674389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv1037713	chr15:75401213-75665304	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv482859	chr15:75493899-75688451	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
4	nsv1035829	chr15:75504534-75692417	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv977736	chr15:75509295-75632679	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
7	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
8	nsv530345	chr15:75628556-75951011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs3809547	MAN2C1	cis	Stomach	GTEx
rs3809547	MAN2C1	cis	Skin Sun Exposed Lower leg	GTEx
rs3809547	MAN2C1	cis	Esophagus Muscularis	GTEx
rs3809547	MAN2C1	cis	Whole Blood	GTEx
rs3809547	MAN2C1	cis	Thyroid	GTEx
rs3809547	MAN2C1	cis	Heart Left Ventricle	GTEx
rs3809547	SNUPN	Cis_1M	lymphoblastoid	RTeQTL
rs3809547	MAN2C1	cis	Esophagus Mucosa	GTEx
rs3809547	MAN2C1	cis	Nerve Tibial	GTEx
rs3809547	MAN2C1	cis	Adipose Subcutaneous	GTEx
rs3809547	MAN2C1	cis	Artery Tibial	GTEx
rs3809547	SNUPN	cis	Thyroid	GTEx
rs3809547	MAN2C1	cis	Artery Aorta	GTEx
rs3809547	MAN2C1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75627600-75629000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr15:75627600-75629400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr15:75627800-75629000	Active TSS	H1 Cell Line	embryonic stem cell
4	chr15:75627800-75629000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:75627800-75629000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:75627800-75629000	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr15:75627800-75629000	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr15:75627800-75629000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:75627800-75629000	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr15:75627800-75629000	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr15:75627800-75629000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:75627800-75629000	Active TSS	Fetal Kidney	kidney
13	chr15:75627800-75629000	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr15:75627800-75629000	Active TSS	NHLF	lung
15	chr15:75627800-75629200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr15:75627800-75629200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:75627800-75629200	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr15:75627800-75629200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr15:75627800-75629200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr15:75627800-75629200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr15:75627800-75629400	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr15:75627800-75629400	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr15:75627800-75629400	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr15:75627800-75629400	Flanking Active TSS	Liver	Liver
25	chr15:75627800-75629600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:75628000-75629000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr15:75628000-75629000	Flanking Active TSS	Primary B cells from peripheral blood	blood
28	chr15:75628000-75629000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr15:75628000-75629000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:75628000-75629000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:75628000-75629000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr15:75628000-75629000	Active TSS	Aorta	Aorta
33	chr15:75628000-75629000	Active TSS	Colon Smooth Muscle	Colon
34	chr15:75628000-75629000	Active TSS	Esophagus	oesophagus
35	chr15:75628000-75629000	Active TSS	Fetal Heart	heart
36	chr15:75628000-75629000	Active TSS	Fetal Intestine Small	intestine
37	chr15:75628000-75629000	Active TSS	A549	lung
38	chr15:75628000-75629000	Active TSS	HepG2	liver
39	chr15:75628000-75629000	Active TSS	K562	blood
40	chr15:75628000-75629000	Active TSS	NHDF-Ad	bronchial
41	chr15:75628000-75629200	Active TSS	H9 Cell Line	embryonic stem cell
42	chr15:75628000-75629200	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr15:75628000-75629200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:75628000-75629600	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr15:75628200-75629000	Active TSS	Fetal Lung	lung
46	chr15:75628200-75629400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr15:75628400-75629000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr15:75628400-75629000	Active TSS	Small Intestine	intestine
49	chr15:75628400-75629200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr15:75628400-75629200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links