Variant report

Variant	rs11119309
Chromosome Location	chr1:209742782-209742783
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	RAD21	chr1:209742714-209743109	MCF-7	breast:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
2	RAD21	chr1:209742738-209743197	MCF-7	breast:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
3	CTCF	chr1:209742749-209743171	HepG2	liver:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
4	CTCF	chr1:209742767-209743211	HCT-116	colon:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
5	CTCF	chr1:209742765-209743197	GM12878	blood:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
6	RAD21	chr1:209742566-209743562	SK-N-SH	brain:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
7	CTCF	chr1:209742697-209743234	K562	blood:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
8	SMC3	chr1:209742535-209743391	SK-N-SH	brain:	n/a	chr1:209742967-209742981
9	RAD21	chr1:209742775-209743191	Hela-S3	cervix:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
10	CTCF	chr1:209742747-209743115	H1-hESC	embryonic stem cell:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
11	CTCF	chr1:209742777-209743156	ECC-1	luminal epithelium:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
12	CTCF	chr1:209742738-209743127	K562	blood:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
13	CTCF	chr1:209742755-209743128	A549	lung:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
14	RAD21	chr1:209742712-209743240	A549	lung:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
15	RAD21	chr1:209742726-209743380	HCT-116	colon:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
16	CTCF	chr1:209742479-209743485	A549	lung:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
17	CTCF	chr1:209742574-209743752	SK-N-SH	brain:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
18	SMC3	chr1:209742776-209743388	GM12878	blood:	n/a	chr1:209742967-209742981
19	RAD21	chr1:209742702-209743267	ECC-1	luminal epithelium:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
20	CTCF	chr1:209742744-209743157	A549	lung:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
21	CBX3	chr1:209742712-209743308	HCT-116	colon:	n/a	n/a
22	CTCF	chr1:209742547-209743179	IMR90	lung:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
23	RAD21	chr1:209742688-209743288	A549	lung:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
24	CTCF	chr1:209742604-209743189	K562	blood:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
25	RAD21	chr1:209742769-209743167	H1-hESC	embryonic stem cell:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
26	RAD21	chr1:209742751-209743160	IMR90	lung:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
27	CTCF	chr1:209742778-209743144	SK-N-SH_RA	brain:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
28	CTCF	chr1:209742770-209743178	A549	lung:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
29	RAD21	chr1:209742730-209743241	H1-hESC	embryonic stem cell:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
30	RAD21	chr1:209742657-209743320	HCT-116	colon:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
31	RAD21	chr1:209742776-209743166	HepG2	liver:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
32	CTCF	chr1:209742700-209743132	MCF-7	breast:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
33	CTCF	chr1:209742595-209743416	HCT-116	colon:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982

No.	Distal block	Cell Line	Cell type
1	chr1:209742599..209743311-chr1:209800709..209801256,2	MCF-7	breast:
2	chr1:209742327..209743226-chr1:209920951..209921587,3	MCF-7	breast:
3	chr1:209742263..209743556-chr1:209920676..209921449,8	K562	blood:
4	chr1:209742622..209744127-chr1:209864930..209867210,2	MCF-7	breast:
5	chr1:209742477..209743064-chr1:209800705..209801620,3	K562	blood:
6	chr1:209742414..209743881-chr1:209865939..209867133,12	K562	blood:

Variant related genes	Relation type
ENSG00000224260	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10489338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119308	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12058586	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs12069172	0.83[ASN][1000 genomes]
rs12074063	0.91[ASN][1000 genomes]
rs12080730	0.83[ASN][1000 genomes]
rs12094286	0.81[ASN][1000 genomes]
rs12410975	1.00[MKK][hapmap]
rs17014758	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17014770	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17014799	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17014808	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17014825	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17014842	0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs2067744	0.83[ASN][1000 genomes]
rs2072908	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs2076225	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs60686175	0.84[ASN][1000 genomes]
rs6663545	0.83[ASN][1000 genomes]
rs6690557	0.95[CHB][hapmap]
rs7512091	0.85[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs926385	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9429821	0.95[CHB][hapmap]
rs9429822	0.83[ASN][1000 genomes]
rs9430000	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs9430001	1.00[CHB][hapmap]
rs9430005	0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209738400-209743000	Weak transcription	Fetal Kidney	kidney
2	chr1:209739600-209743000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:209739800-209743000	Weak transcription	Brain Substantia Nigra	brain
4	chr1:209741200-209743000	Weak transcription	Osteobl	bone
5	chr1:209741200-209743200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:209741200-209743600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:209741400-209743400	Enhancers	NHEK	skin
8	chr1:209741600-209743000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:209741600-209743000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:209741600-209743000	Weak transcription	HSMM	muscle
11	chr1:209741800-209743000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:209741800-209743000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr1:209742000-209743000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:209742000-209743000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:209742400-209742800	Weak transcription	HMEC	breast
16	chr1:209742400-209743000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:209742600-209743400	Enhancers	Primary T killer memory cells from peripheral blood	blood

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