Variant report

Variant	rs4752845
Chromosome Location	chr11:47539697-47539698
allele	C/T
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	IRF1	chr11:47539568-47539769	K562	blood:	n/a	chr11:47539568-47539577 chr11:47539717-47539724
2	POLR2A	chr11:47539672-47540436	H1-neurons	neurons:	n/a	n/a
3	FOXA2	chr11:47539659-47539928	HepG2	liver:	n/a	n/a
4	POLR2A	chr11:47539643-47539719	MCF-7	breast:	n/a	n/a
5	POLR2A	chr11:47539676-47540174	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:47538256..47540735-chr11:47545712..47549245,3	K562	blood:
2	chr11:47539127..47541953-chr11:47544239..47547576,3	MCF-7	breast:
3	chr11:47537508..47540413-chr11:47573164..47576003,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270072	TF binding region
ENSG00000149187	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1057233	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs1064608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10742803	0.88[CEU][hapmap];0.82[ASN][1000 genomes]
rs10769258	0.89[CEU][hapmap];0.90[CHB][hapmap]
rs10769262	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs10838698	0.89[CEU][hapmap];0.90[CHB][hapmap]
rs10838699	0.89[CEU][hapmap];0.91[CHB][hapmap]
rs10838704	0.81[ASN][1000 genomes]
rs10838706	0.81[ASN][1000 genomes]
rs10838708	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10838724	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10838738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10838747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs10838748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11039212	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs11039219	0.81[ASN][1000 genomes]
rs11039238	0.88[ASN][1000 genomes]
rs11039255	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039265	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11039307	0.81[ASN][1000 genomes]
rs11570094	1.00[YRI][hapmap]
rs11600581	0.81[ASN][1000 genomes]
rs11601603	0.89[CEU][hapmap]
rs11604680	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11605672	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs12419692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12787112	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs12794570	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12798028	0.82[ASN][1000 genomes]
rs12798346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs1317149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2030166	0.82[ASN][1000 genomes]
rs2053979	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2071304	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs2293577	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2293578	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2293580	0.82[ASN][1000 genomes]
rs2856650	1.00[YRI][hapmap]
rs2868459	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs34958982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35184771	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35496532	0.83[ASN][1000 genomes]
rs35705029	0.89[ASN][1000 genomes]
rs3781624	0.82[ASN][1000 genomes]
rs3781625	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3781626	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3781627	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3817334	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3817335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4752838	0.89[ASN][1000 genomes]
rs4752856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4752857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4752990	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs4752993	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs4752994	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs4752999	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4992357	0.88[CEU][hapmap];0.95[CHB][hapmap]
rs55927797	0.82[ASN][1000 genomes]
rs56400411	0.84[ASN][1000 genomes]
rs60075622	0.82[ASN][1000 genomes]
rs6485753	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs66749409	0.85[ASN][1000 genomes]
rs7106956	0.89[ASN][1000 genomes]
rs7107726	0.81[ASN][1000 genomes]
rs7124681	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs755553	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs755554	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs755555	0.81[ASN][1000 genomes]
rs7925389	0.88[ASN][1000 genomes]
rs7928842	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7937331	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7940536	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs896816	0.89[CEU][hapmap];0.95[CHB][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	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers 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 miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4752845	C1QTNF4	cis	Artery Tibial	GTEx
rs4752845	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs4752845	SPI1	cis	multi-tissue	Pritchard
rs4752845	C1QTNF4	cis	multi-tissue	Pritchard
rs4752845	C1QTNF4	cis	lung	GTEx
rs4752845	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs4752845	C1QTNF4	cis	Muscle Skeletal	GTEx
rs4752845	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs4752845	Hs.6637	cis	multi-tissue	Pritchard
rs4752845	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs4752845	C1QTNF4	cis	Whole Blood	GTEx
rs4752845	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47523000-47545600	Weak transcription	Dnd41	blood
2	chr11:47524800-47549600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr11:47528400-47544800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr11:47528800-47541000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr11:47530200-47543000	Enhancers	Primary T cells fromperipheralblood	blood
6	chr11:47531200-47540400	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr11:47531600-47542000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr11:47532000-47539800	Weak transcription	Fetal Intestine Large	intestine
9	chr11:47532400-47540600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr11:47533400-47540800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr11:47533800-47539800	Weak transcription	Fetal Stomach	stomach
12	chr11:47534400-47539800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr11:47534400-47541400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:47535000-47540600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr11:47535000-47544600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:47535600-47539800	Enhancers	Primary T cells from cord blood	blood
17	chr11:47535600-47540000	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr11:47535600-47540600	Enhancers	Brain Hippocampus Middle	brain
19	chr11:47535600-47540800	Enhancers	Liver	Liver
20	chr11:47535600-47541200	Enhancers	Lung	lung
21	chr11:47535600-47545200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr11:47535800-47540800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr11:47535800-47541000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr11:47535800-47541000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:47536000-47540200	Enhancers	Fetal Brain Male	brain
26	chr11:47536000-47542000	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr11:47536200-47541600	Enhancers	Left Ventricle	heart
28	chr11:47536400-47539800	Enhancers	Colon Smooth Muscle	Colon
29	chr11:47536800-47539800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr11:47536800-47542400	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr11:47537000-47539800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:47537000-47540200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:47537000-47540200	Weak transcription	Aorta	Aorta
34	chr11:47537000-47540200	Weak transcription	Colonic Mucosa	Colon
35	chr11:47537000-47540600	Enhancers	Brain Cingulate Gyrus	brain
36	chr11:47537000-47541000	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr11:47537000-47541000	Enhancers	Adipose Nuclei	Adipose
38	chr11:47537000-47545000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr11:47537200-47539800	Weak transcription	Brain Angular Gyrus	brain
40	chr11:47537200-47540000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr11:47537200-47540200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr11:47537200-47540200	Weak transcription	Ovary	ovary
43	chr11:47537200-47541000	Enhancers	Primary B cells from peripheral blood	blood
44	chr11:47537200-47542400	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr11:47537200-47544800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr11:47537200-47545000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:47537200-47545000	Weak transcription	Esophagus	oesophagus
48	chr11:47537200-47545000	Weak transcription	Pancreas	Pancrea
49	chr11:47537400-47539800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr11:47537400-47539800	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links