Variant report

Variant	rs4542419
Chromosome Location	chr11:66970597-66970598
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	FOS	chr11:66970520-66970731	MCF10A-Er-Src	breast:	n/a	chr11:66970617-66970628
2	FOS	chr11:66970523-66970732	MCF10A-Er-Src	breast:	n/a	chr11:66970617-66970628
3	FOS	chr11:66970486-66970768	MCF10A-Er-Src	breast:	n/a	chr11:66970617-66970628
4	JUN	chr11:66970515-66970772	Hela-S3	cervix:	n/a	n/a
5	JUND	chr11:66970500-66970772	Hela-S3	cervix:	n/a	n/a
6	FOS	chr11:66970531-66970789	MCF10A-Er-Src	breast:	n/a	chr11:66970617-66970628
7	FOS	chr11:66970486-66970761	HUVEC	blood vessel:	n/a	chr11:66970617-66970628
8	EP300	chr11:66970584-66970777	Hela-S3	cervix:	n/a	n/a
9	CEBPB	chr11:66970429-66970738	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66962013..66964416-chr11:66967953..66970600,2	MCF-7	breast:
2	chr11:66970095..66972335-chr11:66976839..66979350,2	K562	blood:

Variant related genes	Relation type
KDM2A	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10896154	0.92[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs10896167	0.92[ASW][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes]
rs11227756	1.00[ASW][hapmap];0.90[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs11601700	0.84[EUR][1000 genomes]
rs12288048	0.87[GIH][hapmap]
rs1253778	0.88[AMR][1000 genomes]
rs12788752	0.92[ASW][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.81[MKK][hapmap];0.93[YRI][hapmap]
rs1638566	0.92[ASW][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs1638567	0.92[ASW][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs1638571	0.92[ASW][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs1790740	0.92[ASW][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs2001635	0.92[ASW][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];0.91[MKK][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes]
rs2001636	0.83[AMR][1000 genomes]
rs2066496	0.84[CHD][hapmap]
rs2071007	1.00[ASW][hapmap];0.90[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2256154	0.92[CHD][hapmap]
rs2286620	0.84[CHD][hapmap]
rs3758943	0.83[CHB][hapmap];0.84[JPT][hapmap];0.93[YRI][hapmap]
rs3781941	0.92[ASW][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs3781942	0.92[ASW][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs3781943	0.92[ASW][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap]
rs3927807	1.00[ASW][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.97[MKK][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4244819	1.00[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4255546	0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[TSI][hapmap]
rs4375446	1.00[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4478996	1.00[ASW][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4503557	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4930192	0.83[CHD][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs4930197	0.92[ASW][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs4930418	0.84[CHD][hapmap];0.90[TSI][hapmap]
rs56337023	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs608273	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs646834	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6591232	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6591239	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs660960	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs674499	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7113390	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7124968	0.86[ASN][1000 genomes]
rs7480390	0.85[JPT][hapmap]
rs7484186	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7930829	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs872110	0.85[ASW][hapmap];0.97[CHD][hapmap];0.80[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap]
rs9943601	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv532287	chr11:66784014-67023899	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66907800-66975000	Weak transcription	Pancreas	Pancrea
2	chr11:66930800-66985600	Weak transcription	Small Intestine	intestine
3	chr11:66936400-67006200	Weak transcription	Stomach Mucosa	stomach
4	chr11:66942600-66982800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:66945800-66984800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr11:66948000-66970600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr11:66948200-66975000	Weak transcription	Right Ventricle	heart
8	chr11:66948200-66986400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:66949600-66975000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr11:66951200-66975000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr11:66951200-66975000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr11:66951200-66986600	Weak transcription	Fetal Brain Male	brain
13	chr11:66953000-66975000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr11:66953400-66982800	Weak transcription	Aorta	Aorta
15	chr11:66953400-66982800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:66953800-66978400	Weak transcription	K562	blood
17	chr11:66953800-66982800	Weak transcription	HUVEC	blood vessel
18	chr11:66954000-66974600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr11:66954000-66976000	Weak transcription	Brain Substantia Nigra	brain
20	chr11:66954000-66979400	Weak transcription	Brain Hippocampus Middle	brain
21	chr11:66954000-66984800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr11:66954400-66974600	Weak transcription	Brain Germinal Matrix	brain
23	chr11:66954600-66993000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr11:66954800-66975000	Weak transcription	Colon Smooth Muscle	Colon
25	chr11:66956000-66975000	Weak transcription	Spleen	Spleen
26	chr11:66956400-67005000	Weak transcription	Fetal Heart	heart
27	chr11:66962200-66999000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:66962400-66982800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr11:66962600-66972600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr11:66962600-66974400	Weak transcription	NH-A	brain
31	chr11:66962600-66995000	Weak transcription	Psoas Muscle	Psoas
32	chr11:66962800-66977400	Weak transcription	Esophagus	oesophagus
33	chr11:66963800-66974400	Weak transcription	NHLF	lung
34	chr11:66963800-66978400	Weak transcription	HSMMtube	muscle
35	chr11:66963800-66980400	Weak transcription	A549	lung
36	chr11:66964000-66975000	Weak transcription	Left Ventricle	heart
37	chr11:66964000-66975000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr11:66964000-66982800	Weak transcription	NHEK	skin
39	chr11:66964200-66975000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr11:66964400-66989400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:66964600-67002400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr11:66965200-66974800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr11:66965200-66978200	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr11:66965200-67006400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr11:66965400-66975000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr11:66965400-66982800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr11:66965800-66970800	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr11:66965800-66974200	Weak transcription	Fetal Kidney	kidney
49	chr11:66965800-66974800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr11:66965800-66975000	Weak transcription	HSMM	muscle

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