Variant report

Variant	rs519473
Chromosome Location	chr11:62647213-62647214
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	POLR2A	chr11:62647110-62659411	PFSK-1	brain:	n/a	n/a
2	JUN	chr11:62647023-62650673	K562	blood:	n/a	chr11:62649835-62649844 chr11:62650315-62650324 chr11:62649133-62649141 chr11:62649134-62649145 chr11:62649132-62649142 chr11:62649132-62649142 chr11:62648147-62648161 chr11:62649206-62649219 chr11:62649132-62649142 chr11:62649131-62649143
3	POLR2A	chr11:62646624-62655022	SK-N-MC	brain:	n/a	n/a
4	NR3C1	chr11:62647056-62647400	ECC-1	luminal epithelium:	n/a	chr11:62647240-62647261 chr11:62647242-62647258 chr11:62647243-62647257 chr11:62647243-62647257 chr11:62647242-62647258 chr11:62647242-62647258
5	POLR2A	chr11:62647114-62647419	HUVEC	blood vessel:	n/a	n/a
6	NR3C1	chr11:62646961-62647516	A549	lung:	n/a	chr11:62647240-62647261 chr11:62647242-62647258 chr11:62647243-62647257 chr11:62647243-62647257 chr11:62647242-62647258 chr11:62647242-62647258
7	NR3C1	chr11:62647033-62647448	ECC-1	luminal epithelium:	n/a	chr11:62647240-62647261 chr11:62647242-62647258 chr11:62647243-62647257 chr11:62647243-62647257 chr11:62647242-62647258 chr11:62647242-62647258
8	MXI1	chr11:62647118-62649962	SK-N-SH	brain:	n/a	chr11:62649551-62649566
9	JUND	chr11:62646604-62649773	SK-N-SH	brain:	n/a	chr11:62649133-62649141 chr11:62649131-62649142 chr11:62649134-62649145 chr11:62649132-62649142 chr11:62649132-62649142 chr11:62648147-62648161 chr11:62649132-62649142 chr11:62649131-62649143
10	CTCF	chr11:62647200-62647350	GM12865	blood:	n/a	n/a
11	NR3C1	chr11:62647084-62647459	A549	lung:	n/a	chr11:62647240-62647261 chr11:62647242-62647258 chr11:62647243-62647257 chr11:62647243-62647257 chr11:62647242-62647258 chr11:62647242-62647258
12	POLR2A	chr11:62646726-62649799	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr11:62647080-62647230	SK-N-SH_RA	brain:	n/a	n/a
14	NR3C1	chr11:62647070-62647408	A549	lung:	n/a	chr11:62647240-62647261 chr11:62647242-62647258 chr11:62647243-62647257 chr11:62647243-62647257 chr11:62647242-62647258 chr11:62647242-62647258
15	POLR2A	chr11:62647162-62647365	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr11:62647160-62647310	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr11:62646998-62647483	HepG2	liver:	n/a	n/a
18	CTCF	chr11:62647180-62647330	AG04449	skin:	n/a	n/a
19	POLR2A	chr11:62646772-62659196	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr11:62647180-62647330	HepG2	liver:	n/a	n/a
21	GATA1	chr11:62646618-62647485	PBDE	blood:	n/a	chr11:62646931-62646938 chr11:62646932-62646949 chr11:62646929-62646941 chr11:62646931-62646938 chr11:62646930-62646940 chr11:62646931-62646938
22	CTCF	chr11:62647140-62647290	SK-N-SH_RA	brain:	n/a	n/a
23	POLR2A	chr11:62647190-62649667	K562	blood:	n/a	n/a
24	MAX	chr11:62647106-62649828	HCT-116	colon:	n/a	chr11:62649208-62649217 chr11:62649557-62649566

No.	Distal block	Cell Line	Cell type
1	chr11:62357563..62359095-chr11:62646957..62649775,2	K562	blood:
2	chr11:62436644..62439359-chr11:62646545..62649165,3	MCF-7	breast:
3	chr11:62520275..62522946-chr11:62645985..62649381,3	K562	blood:
4	chr11:62492683..62497467-chr11:62646838..62651892,11	MCF-7	breast:
5	chr11:62568262..62574296-chr11:62646831..62652869,25	K562	blood:
6	chr11:62492996..62496945-chr11:62646247..62651278,7	K562	blood:
7	chr11:62367640..62370552-chr11:62646699..62650475,4	K562	blood:
8	chr11:62521216..62523210-chr11:62647073..62650275,3	MCF-7	breast:
9	chr11:62570028..62574835-chr11:62645876..62651719,9	MCF-7	breast:
10	chr11:62646885..62648514-chr7:148821203..148823858,2	MCF-7	breast:
11	chr11:62614063..62631836-chr11:62641578..62658963,131	K562	blood:
12	chr11:62647065..62649717-chr20:58515490..58517271,2	MCF-7	breast:
13	chr11:62537178..62539067-chr11:62647194..62649874,3	MCF-7	breast:
14	chr11:62597102..62625754-chr11:62640222..62672995,305	MCF-7	breast:
15	chr11:62645804..62648522-chr12:133562375..133564190,2	MCF-7	breast:
16	chr11:62432088..62434387-chr11:62647031..62649538,2	MCF-7	breast:
17	chr11:62437394..62440869-chr11:62646713..62650476,3	MCF-7	breast:
18	chr11:62552792..62555847-chr11:62647130..62649597,5	MCF-7	breast:
19	chr11:62645443..62647848-chr11:63974874..63976956,2	K562	blood:
20	chr11:62551512..62560180-chr11:62645894..62651775,24	K562	blood:
21	chr11:62596557..62612020-chr11:62639561..62665043,131	K562	blood:
22	chr11:62444978..62447315-chr11:62646743..62649778,3	K562	blood:

Variant related genes	Relation type
SLC3A2	TF binding region
ENSG00000269176	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000162227	Chromatin interaction
ENSG00000185670	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000197024	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000149781	Chromatin interaction
ENSG00000162231	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000256690	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000198393	Chromatin interaction
ENSG00000196227	Chromatin interaction
ENSG00000162191	Chromatin interaction
ENSG00000149480	Chromatin interaction
ENSG00000204922	Chromatin interaction
ENSG00000240877	Chromatin interaction
ENSG00000162236	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000204947	Chromatin interaction
ENSG00000168569	Chromatin interaction
ENSG00000185475	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11568617	1.00[AMR][1000 genomes]
rs11568622	1.00[AMR][1000 genomes]
rs11822922	1.00[EUR][1000 genomes]
rs12273912	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1787724	1.00[EUR][1000 genomes]
rs2510538	1.00[EUR][1000 genomes]
rs2584915	0.83[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2584917	1.00[EUR][1000 genomes]
rs2730030	1.00[EUR][1000 genomes]
rs2956139	1.00[EUR][1000 genomes]
rs2958240	1.00[EUR][1000 genomes]
rs481272	0.94[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs482331	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];1.00[EUR][1000 genomes]
rs486451	0.83[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs489275	1.00[EUR][1000 genomes]
rs4963309	0.83[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs506132	1.00[EUR][1000 genomes]
rs507101	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs514401	1.00[EUR][1000 genomes]
rs518780	1.00[EUR][1000 genomes]
rs523328	1.00[EUR][1000 genomes]
rs544573	1.00[EUR][1000 genomes]
rs560006	0.84[YRI][hapmap];0.85[AFR][1000 genomes]
rs560603	0.82[AFR][1000 genomes]
rs560618	1.00[EUR][1000 genomes]
rs561385	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56226867	1.00[EUR][1000 genomes]
rs56262657	1.00[EUR][1000 genomes]
rs564587	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs572513	0.83[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs573146	1.00[EUR][1000 genomes]
rs57338459	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs575134	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs577071	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57858466	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs592337	1.00[EUR][1000 genomes]
rs595108	1.00[EUR][1000 genomes]
rs60568977	1.00[EUR][1000 genomes]
rs60668695	1.00[EUR][1000 genomes]
rs619109	1.00[EUR][1000 genomes]
rs646194	1.00[EUR][1000 genomes]
rs692773	1.00[EUR][1000 genomes]
rs694678	1.00[EUR][1000 genomes]
rs73487834	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73487878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73487879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73487880	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73490026	1.00[EUR][1000 genomes]
rs73492003	1.00[AMR][1000 genomes]
rs73492015	1.00[AMR][1000 genomes]
rs73502133	1.00[EUR][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	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers 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	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv1051308	chr11:62564713-62673136	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1199 gene(s)	inside rSNPs	diseases
4	nsv541058	chr11:62564713-62673136	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1199 gene(s)	inside rSNPs	diseases
5	nsv1041770	chr11:62610353-62871767	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	263 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs519473	C11orf48	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62630800-62648400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:62631600-62648200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:62638400-62647400	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr11:62640800-62647400	Weak transcription	Primary T cells from cord blood	blood
5	chr11:62641600-62647400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr11:62643000-62647400	Weak transcription	Fetal Kidney	kidney
7	chr11:62643000-62647800	Enhancers	Pancreas	Pancrea
8	chr11:62645000-62647800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr11:62645600-62647600	Enhancers	Lung	lung
10	chr11:62646400-62647400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr11:62646400-62647400	Enhancers	Brain Cingulate Gyrus	brain
12	chr11:62646400-62647600	Enhancers	Ovary	ovary
13	chr11:62646400-62647800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:62646600-62647400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr11:62646600-62647400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr11:62646600-62647400	Enhancers	Psoas Muscle	Psoas
17	chr11:62646600-62647600	Genic enhancers	Fetal Intestine Small	intestine
18	chr11:62646600-62647600	Enhancers	Fetal Muscle Leg	muscle
19	chr11:62646600-62647600	Enhancers	Right Atrium	heart
20	chr11:62646600-62647800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr11:62646800-62647400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr11:62646800-62647400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr11:62646800-62647400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr11:62646800-62647400	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr11:62646800-62647400	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr11:62646800-62647400	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr11:62646800-62647400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr11:62646800-62647400	Enhancers	Brain Angular Gyrus	brain
29	chr11:62646800-62647400	Enhancers	Brain Germinal Matrix	brain
30	chr11:62646800-62647400	Enhancers	Fetal Intestine Large	intestine
31	chr11:62646800-62647400	Enhancers	Left Ventricle	heart
32	chr11:62646800-62647400	Enhancers	Right Ventricle	heart
33	chr11:62646800-62647600	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr11:62646800-62647600	Enhancers	Primary hematopoietic stem cells	blood
35	chr11:62646800-62647600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
36	chr11:62646800-62647600	Enhancers	Aorta	Aorta
37	chr11:62646800-62647600	Enhancers	Colonic Mucosa	Colon
38	chr11:62646800-62647600	Enhancers	Duodenum Mucosa	Duodenum
39	chr11:62646800-62647600	Enhancers	Fetal Muscle Trunk	muscle
40	chr11:62646800-62647600	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr11:62646800-62647800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr11:62646800-62647800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr11:62646800-62647800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:62646800-62647800	Enhancers	Esophagus	oesophagus
45	chr11:62646800-62647800	Enhancers	Gastric	stomach
46	chr11:62646800-62648200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr11:62647000-62647400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr11:62647000-62647400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr11:62647000-62647400	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr11:62647000-62647400	Enhancers	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links