Variant report

Variant	rs2845570
Chromosome Location	chr11:65790527-65790528
allele	G/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	SMC3	chr11:65789748-65790556	SK-N-SH	brain:	n/a	chr11:65790076-65790090
2	CTCF	chr11:65790460-65790610	GM12864	blood:	n/a	n/a
3	CTCF	chr11:65790520-65790670	HAc	cerebellar:	n/a	n/a
4	ELF1	chr11:65789792-65790573	K562	blood:	n/a	chr11:65790139-65790151
5	CTCF	chr11:65789694-65790668	A549	lung:	n/a	chr11:65790075-65790091 chr11:65790074-65790092
6	CTCF	chr11:65789783-65790683	SK-N-SH	brain:	n/a	chr11:65790075-65790091 chr11:65790074-65790092
7	CTCF	chr11:65790420-65790570	GM12872	blood:	n/a	n/a
8	RAD21	chr11:65789724-65790580	SK-N-SH	brain:	n/a	chr11:65790140-65790153
9	CTCF	chr11:65789791-65790540	HCT-116	colon:	n/a	chr11:65790075-65790091 chr11:65790074-65790092

No.	Distal block	Cell Line	Cell type
1	chr11:65756138..65757491-chr11:65789561..65790625,11	MCF-7	breast:
2	chr11:65790040..65790560-chr3:72495787..72496645,3	HCT-116	colon:
3	chr11:65769812..65778104-chr11:65786537..65794453,15	K562	blood:
4	chr11:65788482..65791914-chr11:65833749..65837289,3	MCF-7	breast:
5	chr11:65788506..65790955-chr11:65792237..65795353,3	MCF-7	breast:
6	chr11:65661660..65664635-chr11:65790065..65792086,2	K562	blood:
7	chr11:65790322..65792133-chr11:65817466..65819625,2	MCF-7	breast:
8	chr11:65756240..65757374-chr11:65789632..65790577,5	MCF-7	breast:
9	chr11:65770090..65771007-chr11:65789668..65790582,3	MCF-7	breast:
10	chr11:65756555..65757565-chr11:65789607..65790550,4	K562	blood:
11	chr11:65780150..65780653-chr11:65789668..65790559,2	MCF-7	breast:
12	chr11:65772051..65774698-chr11:65790348..65792220,2	MCF-7	breast:
13	chr11:65788326..65791572-chr11:65817870..65821514,6	MCF-7	breast:
14	chr11:65790060..65790560-chr3:72495795..72496559,3	MCF-7	breast:

Variant related genes	Relation type
CATSPER1	TF binding region
ENSG00000175294	Chromatin interaction
ENSG00000238752	Chromatin interaction
ENSG00000175334	Chromatin interaction
ENSG00000163602	Chromatin interaction
ENSG00000255038	Chromatin interaction
ENSG00000087365	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11227384	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1642958	0.82[ASN][1000 genomes]
rs1783563	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2241303	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.84[ASN][1000 genomes]
rs2430978	0.81[ASN][1000 genomes]
rs2576	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4930170	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs493320	0.80[ASN][1000 genomes]
rs537497	0.83[ASW][hapmap];0.83[YRI][hapmap]
rs539046	0.83[ASW][hapmap];0.83[YRI][hapmap]
rs571374	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.83[YRI][hapmap];0.82[ASN][1000 genomes]
rs576836	0.89[JPT][hapmap];0.87[YRI][hapmap];0.82[ASN][1000 genomes]
rs577013	0.80[ASN][1000 genomes]
rs72932627	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832191	chr11:65632329-65806120	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv897768	chr11:65715210-65842064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
4	nsv897769	chr11:65727799-65828625	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
5	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
6	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2845570	SF3B2	cis	cerebellum	SCAN
rs2845570	SF3B2	cis	Whole Blood	GTEx
rs2845570	RPS6KA4	cis	parietal	SCAN
rs2845570	SLC22A6	cis	cerebellum	SCAN
rs2845570	SF3B2	cis	parietal	SCAN
rs2845570	TBC1D10C	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65783400-65811200	Weak transcription	Aorta	Aorta
2	chr11:65787800-65790600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:65787800-65790600	Enhancers	Spleen	Spleen
4	chr11:65788000-65790600	Enhancers	Primary hematopoietic stem cells	blood
5	chr11:65789400-65790600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr11:65789400-65790600	Enhancers	Placenta	Placenta
7	chr11:65789800-65790600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr11:65789800-65790600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
9	chr11:65789800-65790600	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr11:65789800-65790600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr11:65789800-65790600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr11:65789800-65790600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr11:65789800-65790600	Active TSS	Brain Substantia Nigra	brain
14	chr11:65789800-65790600	Enhancers	Pancreas	Pancrea
15	chr11:65789800-65790600	Flanking Active TSS	A549	lung
16	chr11:65789800-65790600	Flanking Active TSS	K562	blood
17	chr11:65789800-65790800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:65790000-65790600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
19	chr11:65790000-65790600	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr11:65790000-65800800	Weak transcription	HSMMtube	muscle
21	chr11:65790200-65790600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
22	chr11:65790200-65790600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:65790200-65790600	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr11:65790200-65790600	Enhancers	Esophagus	oesophagus
25	chr11:65790200-65790600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr11:65790200-65790600	Flanking Bivalent TSS/Enh	HepG2	liver
27	chr11:65790200-65790600	Flanking Active TSS	Osteobl	bone
28	chr11:65790400-65790600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr11:65790400-65790600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr11:65790400-65790600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr11:65790400-65790600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr11:65790400-65790600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr11:65790400-65790600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
34	chr11:65790400-65790600	Enhancers	Liver	Liver
35	chr11:65790400-65790600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
36	chr11:65790400-65790600	Bivalent Enhancer	Dnd41	blood
37	chr11:65790400-65790600	Active TSS	Hela-S3	cervix
38	chr11:65790400-65790600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
39	chr11:65790400-65812600	Weak transcription	Right Atrium	heart
40	chr11:65790400-65818600	Weak transcription	HSMM	muscle

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