Variant report

Variant	rs10742277
Chromosome Location	chr11:32452925-32452926
allele	C/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	CTCF	chr11:32452788-32452929	Pancreas_OC	pancreas:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
2	USF1	chr11:32452685-32452973	H1-hESC	embryonic stem cell:	n/a	n/a
3	TCF12	chr11:32452489-32453021	H1-hESC	embryonic stem cell:	n/a	chr11:32452878-32452885
4	CTCF	chr11:32452840-32452990	GM12868	blood:	n/a	n/a
5	TEAD4	chr11:32452674-32453018	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr11:32452599-32453034	H1-hESC	embryonic stem cell:	n/a	chr11:32452645-32452657
7	CTCF	chr11:32452798-32452928	GM10248	blood:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
8	SUZ12	chr11:32447620-32453523	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr11:32452780-32452930	GM12864	blood:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
10	CTCF	chr11:32452780-32452930	GM12869	blood:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
11	CHD2	chr11:32452646-32452946	H1-hESC	embryonic stem cell:	n/a	chr11:32452652-32452662
12	CTCF	chr11:32452722-32453005	GM12878	blood:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
13	SP1	chr11:32452625-32452981	H1-hESC	embryonic stem cell:	n/a	n/a
14	TCF12	chr11:32452627-32452937	H1-hESC	embryonic stem cell:	n/a	chr11:32452878-32452885
15	YY1	chr11:32452528-32452937	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr11:32452820-32452970	GM12871	blood:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
17	RAD21	chr11:32452539-32453037	H1-hESC	embryonic stem cell:	n/a	chr11:32452645-32452657
18	CTCF	chr11:32452745-32452937	GM12878	blood:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
19	CTCF	chr11:32452731-32452945	Fibrobl	skin:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
20	CTCF	chr11:32452800-32452950	GM12866	blood:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
21	CTCF	chr11:32452800-32452950	AG09309	skin:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
22	BACH1	chr11:32452728-32452950	H1-hESC	embryonic stem cell:	n/a	n/a
23	RAD21	chr11:32452658-32452962	HepG2	liver:	n/a	n/a
24	CTBP2	chr11:32451694-32453467	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr11:32452820-32452970	GM12872	blood:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
26	CTCF	chr11:32452840-32452990	HUVEC	blood vessel:	n/a	n/a
27	CTCF	chr11:32452740-32452957	GM12891	blood:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
28	POLR2A	chr11:32452050-32453010	K562	blood:	n/a	n/a
29	RAD21	chr11:32452757-32452937	GM12878	blood:	n/a	n/a
30	CTCF	chr11:32452800-32452950	SAEC	small airway:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
31	CTCF	chr11:32452800-32452950	GM12874	blood:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
32	CTCF	chr11:32452768-32452932	HepG2	liver:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
33	CTCF	chr11:32452800-32452950	HPF	lung:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
34	CTCF	chr11:32452609-32452987	H1-hESC	embryonic stem cell:	n/a	chr11:32452838-32452851 chr11:32452660-32452673 chr11:32452836-32452852 chr11:32452835-32452853
35	CTCF	chr11:32452820-32452970	AG04450	lung:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
36	CTCF	chr11:32452800-32452950	HA-sp	spinal cord:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
37	POLR2A	chr11:32452549-32452938	K562	blood:	n/a	n/a
38	CTCF	chr11:32452860-32453010	WERI-Rb-1	eye:	n/a	n/a
39	RAD21	chr11:32452695-32453027	SK-N-SH_RA	brain:	n/a	n/a
40	CTCF	chr11:32452780-32452930	HEEpiC	esophagus:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
41	CTCF	chr11:32452780-32452930	HBMEC	blood vessel:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
42	TEAD4	chr11:32452637-32452936	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr11:32452675-32453028	H1-hESC	embryonic stem cell:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
44	RAD21	chr11:32452642-32453009	HepG2	liver:	n/a	chr11:32452645-32452657
45	CTCF	chr11:32452800-32452950	HMEC	breast:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
46	CTCF	chr11:32452800-32452950	GM06990	blood:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
47	CTCF	chr11:32452744-32452932	GM19239	blood:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
48	CTCF	chr11:32452685-32452966	H1-hESC	embryonic stem cell:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853
49	RAD21	chr11:32452719-32452982	HepG2	liver:	n/a	n/a
50	CTCF	chr11:32452709-32452966	GM19238	blood:	n/a	chr11:32452838-32452851 chr11:32452836-32452852 chr11:32452835-32452853

Variant related genes	Relation type
WT1-AS	TF binding region
WT1	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10835911	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10835916	0.81[AMR][1000 genomes]
rs11031791	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11031792	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11031793	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12270749	0.82[ASN][1000 genomes]
rs2234580	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2301250	0.95[CEU][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2301251	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2301252	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2301253	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2301254	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2418910	0.89[JPT][hapmap];0.84[MEX][hapmap]
rs2900741	0.80[CHD][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap]
rs3087923	0.85[ASN][1000 genomes]
rs3809060	0.95[CEU][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3809061	0.95[CEU][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3809062	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3858446	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3858447	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3858448	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3858454	0.82[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3858455	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3858456	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3886325	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3930317	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3930513	0.91[ASW][hapmap];0.95[CEU][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4140413	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4275604	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4304749	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4980793	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs5030176	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5030178	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5030179	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7103000	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7110547	0.83[ASW][hapmap];0.82[CEU][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7120686	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7395210	0.82[AMR][1000 genomes]
rs7948813	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832108	chr11:32395937-32560583	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1044547	chr11:32435753-32465233	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2753303	chr11:32447324-32494924	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1051559	chr11:32447347-32465233	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10742277	PRR5L	cis	cerebellum	SCAN
rs10742277	WT1AS	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:32448800-32454800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
2	chr11:32450200-32457400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr11:32451200-32453200	Weak transcription	K562	blood
4	chr11:32452000-32453000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr11:32452000-32453000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:32452000-32453000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
7	chr11:32452200-32453000	Bivalent Enhancer	Liver	Liver
8	chr11:32452200-32453200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr11:32452200-32453200	Active TSS	Right Atrium	heart
10	chr11:32452200-32454400	Active TSS	Fetal Kidney	kidney
11	chr11:32452400-32453000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr11:32452400-32453000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr11:32452400-32453000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr11:32452400-32453000	Bivalent Enhancer	HMEC	breast
15	chr11:32452600-32453000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr11:32452600-32453000	Bivalent Enhancer	Adipose Nuclei	Adipose
17	chr11:32452600-32453000	Bivalent Enhancer	Placenta	Placenta
18	chr11:32452600-32453000	Bivalent Enhancer	Fetal Thymus	thymus
19	chr11:32452600-32453000	Bivalent Enhancer	Left Ventricle	heart
20	chr11:32452600-32453000	Bivalent Enhancer	Lung	lung
21	chr11:32452600-32453400	Active TSS	Right Ventricle	heart
22	chr11:32452600-32454200	Flanking Active TSS	Ovary	ovary
23	chr11:32452800-32453000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
24	chr11:32452800-32453000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:32452800-32453000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
26	chr11:32452800-32453000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:32452800-32453200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
28	chr11:32452800-32453600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:32452800-32454400	Weak transcription	Pancreas	Pancrea
30	chr11:32452800-32454800	Weak transcription	Gastric	stomach

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