Variant report

Variant	rs11039149
Chromosome Location	chr11:47276675-47276676
allele	A/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	REST	chr11:47276256-47276811	PFSK-1	brain:	n/a	n/a
2	YY1	chr11:47276340-47276793	HepG2	liver:	n/a	n/a
3	EP300	chr11:47276298-47276743	HepG2	liver:	n/a	n/a
4	HNF4A	chr11:47276273-47277066	HepG2	liver:	n/a	chr11:47276954-47276966 chr11:47276960-47276975 chr11:47276954-47276967 chr11:47276953-47276968 chr11:47276953-47276968 chr11:47276960-47276975 chr11:47276953-47276967 chr11:47276951-47276969 chr11:47276953-47276968 chr11:47276953-47276968 chr11:47276952-47276967 chr11:47276953-47276967 chr11:47276954-47276966 chr11:47276954-47276966 chr11:47276953-47276966
5	SP1	chr11:47276254-47277065	HepG2	liver:	n/a	chr11:47276307-47276321
6	POLR2A	chr11:47276165-47276837	HUVEC	blood vessel:	n/a	n/a
7	FOXP2	chr11:47276340-47276824	PFSK-1	brain:	n/a	n/a
8	TBP	chr11:47276546-47276719	HepG2	liver:	n/a	n/a
9	EP300	chr11:47276440-47276754	HepG2	liver:	n/a	n/a
10	ELF1	chr11:47276298-47276762	HepG2	liver:	n/a	chr11:47276547-47276558 chr11:47276546-47276559
11	POLR2A	chr11:47276037-47277064	PFSK-1	brain:	n/a	n/a
12	FOXP2	chr11:47276268-47276827	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr11:47276303-47276809	HUVEC	blood vessel:	n/a	n/a
14	HEY1	chr11:47276241-47276896	HepG2	liver:	n/a	n/a
15	EP300	chr11:47276372-47276706	SK-N-SH_RA	brain:	n/a	n/a
16	POLR2A	chr11:47276250-47276991	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr11:47276304-47276974	HepG2	liver:	n/a	n/a
18	MXI1	chr11:47276402-47276973	HepG2	liver:	n/a	n/a
19	REST	chr11:47276201-47276731	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr11:47276561-47276747	HepG2	liver:	n/a	n/a
21	POLR2A	chr11:47276306-47276885	HepG2	liver:	n/a	n/a
22	MYBL2	chr11:47276259-47276951	HepG2	liver:	n/a	n/a
23	ELF1	chr11:47276332-47276737	HepG2	liver:	n/a	chr11:47276547-47276558 chr11:47276546-47276559
24	MBD4	chr11:47276237-47277062	HepG2	liver:	n/a	n/a
25	RCOR1	chr11:47276594-47276794	HepG2	liver:	n/a	n/a
26	RXRA	chr11:47276293-47276791	SK-N-SH	brain:	n/a	chr11:47276535-47276542
27	SPI1	chr11:47276243-47276776	HL-60	blood:	n/a	chr11:47276326-47276333
28	NFIC	chr11:47276255-47276765	HepG2	liver:	n/a	n/a
29	MBD4	chr11:47276327-47276757	HepG2	liver:	n/a	n/a
30	HEY1	chr11:47276189-47276950	HepG2	liver:	n/a	n/a
31	RXRA	chr11:47276273-47276801	HepG2	liver:	n/a	chr11:47276535-47276542
32	MAZ	chr11:47275226-47277002	IMR90	lung:	n/a	chr11:47276524-47276533 chr11:47275359-47275368
33	NFIC	chr11:47276304-47276996	HepG2	liver:	n/a	n/a
34	MYBL2	chr11:47276176-47277150	HepG2	liver:	n/a	n/a
35	POLR2A	chr11:47276207-47276883	HepG2	liver:	n/a	n/a
36	POLR2A	chr11:47276291-47276814	HepG2	liver:	n/a	n/a
37	MYC	chr11:47276554-47276688	GM12878	blood:	n/a	n/a
38	POLR2A	chr11:47275834-47277056	HepG2	liver:	n/a	n/a
39	RXRA	chr11:47276177-47276913	HepG2	liver:	n/a	chr11:47276535-47276542
40	ARID3A	chr11:47276372-47276714	HepG2	liver:	n/a	n/a
41	TAF1	chr11:47276254-47276863	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:47236362..47238989-chr11:47273774..47276751,3	K562	blood:
2	chr11:47274831..47277970-chr11:47278025..47280120,3	K562	blood:
3	chr11:47273867..47276931-chr11:47289002..47291937,3	MCF-7	breast:
4	chr11:47206818..47208802-chr11:47275094..47276860,2	MCF-7	breast:
5	chr11:47265054..47272453-chr11:47272862..47282933,17	MCF-7	breast:
6	chr11:47269243..47272486-chr11:47273981..47276768,5	MCF-7	breast:
7	chr11:47275155..47277753-chr11:47277972..47280489,3	MCF-7	breast:
8	chr11:47275538..47277558-chr11:47290062..47292106,2	K562	blood:
9	chr11:47268932..47273259-chr11:47273972..47277777,9	K562	blood:

Variant related genes	Relation type
NR1H3	TF binding region
ENSG00000134575	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000134574	Chromatin interaction
ENSG00000025434	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10501320	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs10838696	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.94[ASN][1000 genomes]
rs10838703	0.81[MEX][hapmap]
rs11039114	1.00[ASW][hapmap]
rs11039130	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs11039138	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs11039139	0.94[ASN][1000 genomes]
rs11039154	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11039159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11039162	0.83[ASN][1000 genomes]
rs11039165	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11039182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039183	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[ASN][1000 genomes]
rs11606287	0.81[MEX][hapmap]
rs11606683	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];0.83[ASN][1000 genomes]
rs11988	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs12361415	0.82[MEX][hapmap]
rs2167080	0.94[ASN][1000 genomes]
rs2596407	0.94[ASN][1000 genomes]
rs2697923	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2856653	0.94[ASN][1000 genomes]
rs749067	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.83[ASN][1000 genomes]
rs7944419	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7944584	0.90[EUR][1000 genomes];1.00[ASN][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	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11039149	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs11039149	MADD	cis	parietal	SCAN
rs11039149	TP53I11	cis	parietal	SCAN
rs11039149	OR4B1	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47271000-47280800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47271400-47278600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:47271400-47278600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:47271400-47278600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:47271400-47278600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr11:47271400-47278600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:47271400-47278800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:47271400-47278800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr11:47271400-47278800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:47271400-47278800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr11:47271400-47278800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr11:47271400-47278800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:47271400-47278800	Weak transcription	Esophagus	oesophagus
14	chr11:47271400-47279000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:47271400-47279000	Weak transcription	Fetal Brain Female	brain
16	chr11:47271400-47279000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr11:47271400-47279200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr11:47271400-47281000	Weak transcription	Thymus	Thymus
19	chr11:47271400-47281200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr11:47271400-47281200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr11:47271400-47281200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr11:47271400-47281200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr11:47271600-47279000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr11:47272000-47278600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:47272400-47286400	Weak transcription	Dnd41	blood
26	chr11:47274600-47277000	Enhancers	Lung	lung
27	chr11:47274800-47276800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr11:47274800-47277000	Enhancers	Hela-S3	cervix
29	chr11:47275000-47276800	Enhancers	HSMMtube	muscle
30	chr11:47275000-47277000	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr11:47275000-47277000	Enhancers	Left Ventricle	heart
32	chr11:47275000-47277000	Enhancers	Pancreas	Pancrea
33	chr11:47275000-47277000	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr11:47275000-47277000	Enhancers	Small Intestine	intestine
35	chr11:47275000-47277000	Enhancers	Stomach Mucosa	stomach
36	chr11:47275000-47277200	Flanking Active TSS	HepG2	liver
37	chr11:47275200-47276800	Enhancers	Right Ventricle	heart
38	chr11:47275200-47276800	Enhancers	A549	lung
39	chr11:47275200-47277000	Enhancers	Brain Angular Gyrus	brain
40	chr11:47275200-47277000	Enhancers	Spleen	Spleen
41	chr11:47275200-47277200	Enhancers	Fetal Lung	lung
42	chr11:47275200-47277200	Enhancers	HUVEC	blood vessel
43	chr11:47275200-47277400	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr11:47275200-47279000	Enhancers	Fetal Muscle Leg	muscle
45	chr11:47275200-47279000	Enhancers	Right Atrium	heart
46	chr11:47275400-47276800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr11:47275400-47277000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:47275400-47277000	Enhancers	Primary hematopoietic stem cells	blood
49	chr11:47275400-47277000	Enhancers	Brain Anterior Caudate	brain
50	chr11:47275400-47277000	Enhancers	Brain Substantia Nigra	brain

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