Variant report

Variant	rs7137455
Chromosome Location	chr12:12664203-12664204
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12662519..12664795-chr12:12714606..12716959,2	K562	blood:
2	chr12:12651288..12653412-chr12:12663902..12666446,2	MCF-7	breast:
3	chr12:12663311..12665385-chr12:12856305..12857896,2	MCF-7	breast:
4	chr12:12652832..12655883-chr12:12662875..12665481,3	MCF-7	breast:
5	chr12:1874559..1877368-chr12:12662625..12665193,2	MCF-7	breast:
6	chr12:12663586..12666811-chr12:12669278..12673958,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10743988	0.93[ASN][1000 genomes]
rs10772570	0.92[CEU][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10845552	0.86[CHB][hapmap]
rs10845559	0.90[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs10845560	0.83[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs10845567	0.94[CHB][hapmap];0.95[ASN][1000 genomes]
rs10845568	0.85[CEU][hapmap]
rs10845572	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]
rs11054937	0.94[ASN][1000 genomes]
rs11054940	0.83[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11054941	0.83[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs11054942	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11054947	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11613385	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12422540	1.00[CHB][hapmap];0.80[JPT][hapmap];0.92[ASN][1000 genomes]
rs1558822	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2041927	0.92[CEU][hapmap]
rs2111271	0.90[CHB][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs2417190	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3815591	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4255620	0.94[ASN][1000 genomes]
rs4763832	0.90[ASN][1000 genomes]
rs4763833	0.94[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7294378	0.86[ASN][1000 genomes]
rs7295305	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.96[ASN][1000 genomes]
rs7295427	0.92[ASN][1000 genomes]
rs7308097	0.94[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7310652	0.94[ASN][1000 genomes]
rs7956984	0.80[CEU][hapmap]
rs7972902	0.94[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs933575	0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs962928	0.83[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7137455	ATF7IP	cis	cerebellum	SCAN
rs7137455	ETV6	cis	cerebellum	SCAN
rs7137455	GUCY2C	cis	cerebellum	SCAN

Chromatin state (count:105 , 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	chr12:12652800-12665000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:12653800-12669000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr12:12654400-12667200	Weak transcription	Primary T cells from cord blood	blood
8	chr12:12656000-12666400	Weak transcription	Spleen	Spleen
9	chr12:12656800-12670800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:12659000-12667000	Weak transcription	Fetal Thymus	thymus
11	chr12:12659000-12669200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr12:12659400-12665200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr12:12659600-12664600	Enhancers	Osteobl	bone
14	chr12:12659600-12665800	Enhancers	Brain Cingulate Gyrus	brain
15	chr12:12659800-12664600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr12:12659800-12664600	Weak transcription	Thymus	Thymus
17	chr12:12659800-12665200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr12:12659800-12665600	Weak transcription	Fetal Intestine Small	intestine
19	chr12:12659800-12667800	Enhancers	Brain Hippocampus Middle	brain
20	chr12:12659800-12669000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr12:12659800-12669800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:12659800-12670800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:12659800-12674200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:12659800-12678600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr12:12660000-12664400	Enhancers	NHDF-Ad	bronchial
26	chr12:12660000-12664600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:12660000-12665000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:12660000-12665200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:12660000-12668600	Enhancers	Brain Substantia Nigra	brain
30	chr12:12660000-12670200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr12:12660000-12681800	Weak transcription	Fetal Kidney	kidney
32	chr12:12660200-12670000	Weak transcription	Fetal Lung	lung
33	chr12:12660400-12664800	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:12660400-12664800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr12:12660400-12665600	Weak transcription	Colon Smooth Muscle	Colon
36	chr12:12660400-12666000	Weak transcription	Placenta	Placenta
37	chr12:12660400-12666400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:12660400-12666400	Weak transcription	Aorta	Aorta
39	chr12:12660400-12667000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:12660400-12669600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr12:12660400-12670000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:12660400-12670000	Weak transcription	HUVEC	blood vessel
43	chr12:12660400-12670600	Weak transcription	Fetal Stomach	stomach
44	chr12:12660400-12672200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr12:12660400-12672400	Weak transcription	Right Ventricle	heart
46	chr12:12660400-12672600	Weak transcription	Esophagus	oesophagus
47	chr12:12660400-12672800	Weak transcription	K562	blood
48	chr12:12660400-12686200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr12:12660600-12667200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:12660800-12665800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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