Variant report

Variant	rs4752791
Chromosome Location	chr11:47736023-47736024
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:47735753-47737363	GM12892	blood:	n/a	n/a
2	MXI1	chr11:47735493-47737290	IMR90	lung:	n/a	chr11:47736668-47736677
3	MTA3	chr11:47735988-47737486	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:47735979-47737415	GM12891	blood:	n/a	n/a
5	POLR2A	chr11:47735940-47737470	PANC-1	pancreas:	n/a	n/a
6	PML	chr11:47735892-47737412	GM12878	blood:	n/a	chr11:47736652-47736660
7	MTA3	chr11:47735802-47737326	GM12878	blood:	n/a	n/a
8	POLR2A	chr11:47736015-47737261	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:47735872-47736698	K562	blood:	n/a	n/a
10	POLR2A	chr11:47735830-47736237	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47734421..47738084-chr11:47868728..47871724,4	K562	blood:
2	chr11:47735244..47736764-chr3:73158620..73160572,2	MCF-7	breast:
3	chr11:47662579..47666117-chr11:47735408..47738256,8	MCF-7	breast:
4	chr11:47735244..47736764-chr17:41464183..41466327,3	K562	blood:
5	chr11:47662583..47667763-chr11:47735291..47739208,6	MCF-7	breast:
6	chr11:47733919..47739426-chr11:47787626..47790588,5	MCF-7	breast:
7	chr11:47735300..47737622-chr11:47868024..47869979,2	MCF-7	breast:

No data

Variant related genes	Relation type
AGBL2	TF binding region
ENSG00000030066	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000109920	Chromatin interaction
ENSG00000109919	Chromatin interaction
ENSG00000223247	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10742816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap]
rs11039387	0.90[ASN][1000 genomes]
rs11819955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs11819979	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11820480	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1474056	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16938631	1.00[ASW][hapmap];0.96[LWK][hapmap];0.92[MKK][hapmap]
rs17791016	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1872167	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2138767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2305982	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2305983	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs2869531	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2869532	0.96[ASN][1000 genomes]
rs4147730	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap]
rs4303192	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4752783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs4752786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4752871	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4752872	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[ASN][1000 genomes]
rs4752877	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4752879	0.89[ASN][1000 genomes]
rs57436966	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58357937	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59205786	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60515486	0.89[ASN][1000 genomes]
rs6485772	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6485774	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs6485783	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6485784	0.90[ASN][1000 genomes]
rs6485788	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7116299	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7120737	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7121264	0.98[ASN][1000 genomes]
rs7124949	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7924699	0.90[ASN][1000 genomes]
rs7927611	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7931089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7939069	1.00[ASW][hapmap];0.82[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs7942031	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7945911	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7952204	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9666924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]

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	nsv469858	chr11:47647515-47837172	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv832143	chr11:47700808-47883540	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4752791	SLC35C1	cis	cerebellum	SCAN
rs4752791	ATG13	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47732400-47737600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:47733000-47736800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr11:47733200-47736200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr11:47733600-47736200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:47735400-47737000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:47735600-47736200	Enhancers	Primary B cells from peripheral blood	blood
7	chr11:47735600-47737200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:47735800-47736200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr11:47735800-47736200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:47735800-47736200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:47735800-47736200	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr11:47735800-47736200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr11:47735800-47736200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr11:47735800-47736200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr11:47735800-47736200	Enhancers	Fetal Thymus	thymus
16	chr11:47735800-47736200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr11:47735800-47736200	Flanking Active TSS	HepG2	liver
18	chr11:47735800-47736200	Enhancers	HMEC	breast
19	chr11:47735800-47736400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr11:47735800-47736400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:47735800-47736400	Flanking Active TSS	Colon Smooth Muscle	Colon
22	chr11:47735800-47736400	Flanking Active TSS	Fetal Lung	lung
23	chr11:47735800-47736400	Enhancers	Small Intestine	intestine
24	chr11:47735800-47736400	Flanking Active TSS	A549	lung
25	chr11:47735800-47736400	Flanking Active TSS	GM12878-XiMat	blood
26	chr11:47735800-47736400	Flanking Active TSS	NHLF	lung
27	chr11:47735800-47736600	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr11:47735800-47736600	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr11:47735800-47736800	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr11:47735800-47737200	Active TSS	K562	blood
31	chr11:47735800-47737400	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr11:47735800-47737400	Flanking Active TSS	Dnd41	blood
33	chr11:47736000-47736200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
34	chr11:47736000-47736200	Enhancers	H9 Cell Line	embryonic stem cell
35	chr11:47736000-47736200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr11:47736000-47736200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr11:47736000-47736200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr11:47736000-47736200	Flanking Active TSS	Brain Angular Gyrus	brain
39	chr11:47736000-47736200	Flanking Active TSS	Brain Anterior Caudate	brain
40	chr11:47736000-47736200	Enhancers	Brain Substantia Nigra	brain
41	chr11:47736000-47736200	Enhancers	Esophagus	oesophagus
42	chr11:47736000-47736200	Enhancers	Fetal Brain Female	brain
43	chr11:47736000-47736200	Enhancers	Fetal Intestine Small	intestine
44	chr11:47736000-47736200	Active TSS	Fetal Muscle Trunk	muscle
45	chr11:47736000-47736200	Enhancers	Fetal Muscle Leg	muscle
46	chr11:47736000-47736200	Enhancers	Fetal Stomach	stomach
47	chr11:47736000-47736200	Enhancers	Left Ventricle	heart
48	chr11:47736000-47736200	Enhancers	Pancreas	Pancrea
49	chr11:47736000-47736200	Enhancers	Psoas Muscle	Psoas
50	chr11:47736000-47736200	Enhancers	Right Atrium	heart

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