Variant report

Variant	rs11552724
Chromosome Location	chr3:49156473-49156474
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49065059..49067026-chr3:49155919..49158301,2	MCF-7	breast:
2	chr3:49056273..49062188-chr3:49155312..49159947,7	K562	blood:
3	chr3:49128926..49138937-chr3:49145476..49160975,31	K562	blood:
4	chr3:49141581..49143765-chr3:49156175..49158476,2	K562	blood:
5	chr3:49058620..49061371-chr3:49155094..49159079,3	MCF-7	breast:
6	chr3:49057812..49061431-chr3:49156444..49158785,4	K562	blood:
7	chr3:49129847..49133782-chr3:49155056..49162049,12	MCF-7	breast:
8	chr3:49151622..49155805-chr3:49155952..49160094,9	K562	blood:
9	chr3:49140522..49142254-chr3:49155638..49159426,3	MCF-7	breast:
10	chr3:49155392..49161176-chr3:49167558..49172640,8	MCF-7	breast:
11	chr3:49154967..49157191-chr3:49202240..49204149,2	MCF-7	breast:
12	chr3:49144707..49154191-chr3:49155059..49160099,12	MCF-7	breast:
13	chr3:49155018..49163811-chr3:49167026..49172599,15	MCF-7	breast:
14	chr3:49148095..49150298-chr3:49155546..49158481,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LAMB2-2	chr3:49156455-49156714	NONHSAT089667

No data

Variant related genes	Relation type
ENSG00000178149	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000172053	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000177352	Chromatin interaction
ENSG00000172046	Chromatin interaction
ENSG00000178035	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10049462	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs10154895	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10865954	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11130184	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1134043	0.92[CEU][hapmap]
rs1134591	1.00[JPT][hapmap]
rs11706052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11706189	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11710247	0.94[EUR][1000 genomes]
rs11712006	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713297	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11715581	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11716334	0.82[ASN][1000 genomes]
rs11716614	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs11717978	0.81[EUR][1000 genomes]
rs11718982	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11719220	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs11719457	0.85[EUR][1000 genomes]
rs11720460	0.91[EUR][1000 genomes]
rs11920267	1.00[JPT][hapmap]
rs12487580	0.80[ASN][1000 genomes]
rs12490393	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12493001	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12629759	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12631989	1.00[JPT][hapmap]
rs12636030	0.89[ASN][1000 genomes]
rs12637037	0.80[ASN][1000 genomes]
rs12637576	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12715434	0.91[EUR][1000 genomes]
rs13064784	0.95[ASN][1000 genomes]
rs13068038	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs13072554	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13077498	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs13080725	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13086240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs13087930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs13090839	0.85[EUR][1000 genomes]
rs13092715	1.00[JPT][hapmap]
rs13096406	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13315711	1.00[JPT][hapmap]
rs2117938	1.00[JPT][hapmap]
rs2304442	1.00[JPT][hapmap]
rs3212	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs34326553	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34343820	0.86[EUR][1000 genomes]
rs34477108	0.80[EUR][1000 genomes]
rs34504524	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34509487	0.85[EUR][1000 genomes]
rs34566463	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs34580506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34784192	0.91[EUR][1000 genomes]
rs34889065	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35060561	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs35102816	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35108630	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35174559	1.00[JPT][hapmap]
rs35185152	0.91[EUR][1000 genomes]
rs35283189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35673421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923475	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4279134	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4308307	0.82[ASN][1000 genomes]
rs4364202	0.93[ASN][1000 genomes]
rs4499638	0.87[ASN][1000 genomes]
rs4513485	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4521268	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4536858	0.87[ASN][1000 genomes]
rs4955410	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4955418	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4955419	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4955420	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4955432	1.00[JPT][hapmap]
rs4974080	1.00[JPT][hapmap]
rs4974082	1.00[JPT][hapmap]
rs5030795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55713230	0.87[ASN][1000 genomes]
rs55921200	0.85[AMR][1000 genomes]
rs56004653	0.81[AMR][1000 genomes]
rs56306491	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56318350	0.85[EUR][1000 genomes]
rs61583136	0.85[ASN][1000 genomes]
rs61729488	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62262517	0.93[ASN][1000 genomes]
rs6414613	1.00[JPT][hapmap]
rs6446196	1.00[CHB][hapmap]
rs6446205	1.00[JPT][hapmap]
rs66991555	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67286839	0.91[EUR][1000 genomes]
rs6770112	0.85[ASN][1000 genomes]
rs6779394	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6781790	1.00[JPT][hapmap]
rs67831908	0.86[EUR][1000 genomes]
rs6784111	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6790914	0.87[ASN][1000 genomes]
rs6794924	0.82[ASN][1000 genomes]
rs6795025	0.87[ASN][1000 genomes]
rs71324929	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71324939	0.91[EUR][1000 genomes]
rs73082362	0.81[AMR][1000 genomes]
rs73084135	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7430198	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7432989	1.00[CHB][hapmap]
rs7615235	0.87[ASN][1000 genomes]
rs7621015	1.00[JPT][hapmap]
rs7626445	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7628719	1.00[JPT][hapmap]
rs7643368	1.00[JPT][hapmap]
rs7652746	1.00[JPT][hapmap]
rs9311439	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs9637481	1.00[JPT][hapmap]
rs9814987	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9826525	0.91[EUR][1000 genomes]
rs9828310	0.91[EUR][1000 genomes]
rs9835439	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9837237	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9837625	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9840050	0.95[ASN][1000 genomes]
rs9844757	1.00[CEU][hapmap]
rs9846123	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9847839	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs9850134	1.00[JPT][hapmap]
rs9850917	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs9855123	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9862483	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9864406	1.00[JPT][hapmap]
rs9880088	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9880309	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs9884022	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9990153	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv876765	chr3:49119063-49160671	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11552724	WDR6	cis	Esophagus Mucosa	GTEx
rs11552724	WDR6	cis	Artery Tibial	GTEx
rs11552724	WDR6	cis	Whole Blood	GTEx
rs11552724	WDR6	cis	Adipose Subcutaneous	GTEx
rs11552724	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs11552724	USP4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49142800-49157200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:49142800-49157600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49143600-49156600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:49143600-49156600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:49143600-49156600	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:49143600-49156600	Strong transcription	Fetal Thymus	thymus
7	chr3:49143600-49156800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:49143800-49156600	Strong transcription	Fetal Muscle Leg	muscle
9	chr3:49143800-49156600	Strong transcription	Osteobl	bone
10	chr3:49144000-49156800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:49144200-49156800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:49144600-49156600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:49144600-49156600	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:49144800-49156600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:49144800-49156600	Strong transcription	Primary T cells from cord blood	blood
16	chr3:49144800-49156800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:49144800-49156800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr3:49145000-49156600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:49145000-49156600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:49145200-49156600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:49145600-49156600	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr3:49145600-49156600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:49146000-49156600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:49146200-49156600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:49146400-49156800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:49147000-49156600	Strong transcription	HSMM	muscle
27	chr3:49148200-49156600	Strong transcription	Thymus	Thymus
28	chr3:49149400-49156600	Strong transcription	Fetal Kidney	kidney
29	chr3:49151000-49156600	Strong transcription	A549	lung
30	chr3:49151400-49156600	Strong transcription	K562	blood
31	chr3:49152600-49156800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
32	chr3:49154000-49156600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
33	chr3:49154200-49156600	Weak transcription	NH-A	brain
34	chr3:49154200-49157000	Genic enhancers	Primary T cells fromperipheralblood	blood
35	chr3:49154800-49156800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr3:49154800-49157000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr3:49155000-49156600	Genic enhancers	Adipose Nuclei	Adipose
38	chr3:49155000-49156800	Genic enhancers	Colon Smooth Muscle	Colon
39	chr3:49155200-49156600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
40	chr3:49155200-49156600	Genic enhancers	Duodenum Smooth Muscle	Duodenum
41	chr3:49155200-49156800	Genic enhancers	Brain Cingulate Gyrus	brain
42	chr3:49155400-49156600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:49155600-49156600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr3:49155600-49156600	Weak transcription	Esophagus	oesophagus
45	chr3:49155600-49156600	Weak transcription	Stomach Mucosa	stomach
46	chr3:49155600-49156600	Weak transcription	Hela-S3	cervix
47	chr3:49155600-49156800	Weak transcription	Small Intestine	intestine
48	chr3:49155600-49157000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr3:49155600-49157200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:49155600-49157200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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