Variant report

Variant	rs10845572
Chromosome Location	chr12:12671104-12671105
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12663586..12666811-chr12:12669278..12673958,4	MCF-7	breast:
2	chr12:12657662..12660778-chr12:12669355..12673750,5	MCF-7	breast:
3	chr12:12669443..12671401-chr12:12739772..12741382,2	MCF-7	breast:
4	chr12:12669920..12672358-chr12:12713747..12715597,2	MCF-7	breast:
5	chr12:12670175..12672490-chr12:12673979..12676406,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10743988	0.90[ASN][1000 genomes]
rs10772570	0.92[CEU][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10845552	0.91[CHB][hapmap]
rs10845559	0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs10845560	0.83[ASW][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs10845567	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs10845568	0.85[CEU][hapmap]
rs11054937	0.91[ASN][1000 genomes]
rs11054940	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11054941	0.83[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs11054942	0.94[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11054947	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11613385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12422540	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs1558822	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2041927	0.92[CEU][hapmap]
rs2111271	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs2417190	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3815591	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4255620	0.91[ASN][1000 genomes]
rs4763832	0.87[ASN][1000 genomes]
rs4763833	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7137455	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7294378	0.84[ASN][1000 genomes]
rs7295305	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap];0.93[ASN][1000 genomes]
rs7295427	0.89[ASN][1000 genomes]
rs7308097	0.91[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs7310652	0.91[ASN][1000 genomes]
rs7956984	0.80[CEU][hapmap]
rs7972902	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs933575	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs962928	0.83[ASW][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758295	chr12:12620654-12783124	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2759880	chr12:12620654-12783124	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv898811	chr12:12655443-12928295	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv523366	chr12:12665246-12679124	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv33583	chr12:12665776-12679108	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10845572	ATF7IP	cis	cerebellum	SCAN
rs10845572	GUCY2C	cis	cerebellum	SCAN
rs10845572	ETV6	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12630800-12681000	Weak transcription	Colonic Mucosa	Colon
2	chr12:12634400-12685200	Weak transcription	Hela-S3	cervix
3	chr12:12639400-12679600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:12641600-12686200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:12659800-12674200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:12659800-12678600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr12:12660000-12681800	Weak transcription	Fetal Kidney	kidney
8	chr12:12660400-12672200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:12660400-12672400	Weak transcription	Right Ventricle	heart
10	chr12:12660400-12672600	Weak transcription	Esophagus	oesophagus
11	chr12:12660400-12672800	Weak transcription	K562	blood
12	chr12:12660400-12686200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:12660800-12672400	Weak transcription	Ovary	ovary
14	chr12:12660800-12676600	Weak transcription	Pancreas	Pancrea
15	chr12:12660800-12679800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:12662200-12672400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr12:12663400-12672400	Weak transcription	HSMMtube	muscle
18	chr12:12663600-12671400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:12663600-12672000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:12664000-12690400	Weak transcription	NHLF	lung
21	chr12:12664600-12672600	Weak transcription	Osteobl	bone
22	chr12:12664800-12673600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:12665000-12671800	Weak transcription	NH-A	brain
24	chr12:12665000-12684400	Weak transcription	NHDF-Ad	bronchial
25	chr12:12665000-12685600	Weak transcription	HMEC	breast
26	chr12:12665000-12686200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:12665200-12671200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr12:12665600-12671600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr12:12665800-12678800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr12:12666800-12681200	Weak transcription	Colon Smooth Muscle	Colon
31	chr12:12667000-12674400	Strong transcription	Fetal Thymus	thymus
32	chr12:12667000-12675000	Weak transcription	Spleen	Spleen
33	chr12:12667200-12673000	Strong transcription	Fetal Muscle Leg	muscle
34	chr12:12667400-12671600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:12667400-12672000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:12667400-12686400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:12667600-12671800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr12:12667600-12671800	Strong transcription	Liver	Liver
39	chr12:12667600-12680800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr12:12667800-12671400	Weak transcription	Primary T cells from cord blood	blood
41	chr12:12668000-12671400	Weak transcription	Fetal Brain Male	brain
42	chr12:12668000-12671800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:12668000-12672400	Weak transcription	Psoas Muscle	Psoas
44	chr12:12668000-12680800	Weak transcription	Right Atrium	heart
45	chr12:12668800-12674200	Strong transcription	Placenta	Placenta
46	chr12:12668800-12674600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr12:12669000-12671200	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr12:12669000-12671400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:12669000-12673000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr12:12669000-12673200	Strong transcription	HepG2	liver

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