Variant report

Variant	rs7279
Chromosome Location	chr12:50523947-50523948
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50512748..50515503-chr12:50523146..50524991,2	MCF-7	breast:
2	chr12:50503233..50504882-chr12:50521389..50523983,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1044370	0.90[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap]
rs10747570	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169294	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11831413	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12426261	0.82[EUR][1000 genomes]
rs12815871	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12824125	0.89[EUR][1000 genomes]
rs12830386	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1862043	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2178173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2358538	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs34573394	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35549836	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35998534	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4459386	0.89[ASW][hapmap];0.89[YRI][hapmap]
rs4883481	0.82[EUR][1000 genomes]
rs56709084	0.86[ASN][1000 genomes]
rs646782	1.00[CHB][hapmap]
rs6580729	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66768395	0.81[ASN][1000 genomes]
rs706791	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.82[TSI][hapmap]
rs706792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs706793	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs7136570	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7294548	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7297421	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301649	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7301740	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302981	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7308356	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7532	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957659	0.89[ASW][hapmap];0.85[LWK][hapmap];0.89[YRI][hapmap]
rs7967705	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7967844	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7972842	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835592	0.80[TSI][hapmap]
rs836170	0.86[ASN][1000 genomes]
rs836171	0.88[ASN][1000 genomes]
rs836172	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs836173	0.84[ASN][1000 genomes]
rs836174	0.84[ASN][1000 genomes]
rs836176	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs836177	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs836179	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs836180	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs836181	0.80[ASN][1000 genomes]
rs844347	0.84[GIH][hapmap]
rs860698	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]

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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7279	SNORA2A	cis	parietal	SCAN
rs7279	LASS5	cis	parietal	SCAN
rs7279	KRT84	cis	cerebellum	SCAN
rs7279	MCRS1	cis	parietal	SCAN
rs7279	DIP2B	cis	cerebellum	SCAN
rs7279	LASS5	cis	cerebellum	SCAN
rs7279	CERS5	cis	Nerve Tibial	GTEx
rs7279	LASS5	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50507000-50537400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:50507000-50539600	Weak transcription	Stomach Mucosa	stomach
3	chr12:50507200-50532000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:50510800-50528400	Strong transcription	Liver	Liver
5	chr12:50511200-50538200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:50511400-50538600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:50512600-50529200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:50512600-50538200	Strong transcription	Primary B cells from cord blood	blood
9	chr12:50516000-50532400	Strong transcription	Duodenum Mucosa	Duodenum
10	chr12:50516600-50536200	Strong transcription	Fetal Intestine Large	intestine
11	chr12:50517600-50548000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:50518000-50532400	Strong transcription	HSMM	muscle
13	chr12:50519200-50524000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:50519200-50538200	Strong transcription	Fetal Muscle Leg	muscle
15	chr12:50519400-50525200	Strong transcription	Colon Smooth Muscle	Colon
16	chr12:50519400-50538400	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr12:50519600-50525000	Strong transcription	Adipose Nuclei	Adipose
18	chr12:50519600-50532600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr12:50519600-50537800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr12:50519600-50538200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr12:50520200-50529400	Strong transcription	Fetal Intestine Small	intestine
22	chr12:50520200-50537800	Strong transcription	Primary T cells from cord blood	blood
23	chr12:50520200-50539000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:50520400-50526400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:50520400-50528400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:50520400-50529800	Strong transcription	Lung	lung
27	chr12:50520400-50530600	Strong transcription	Fetal Stomach	stomach
28	chr12:50520400-50538000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:50520600-50525000	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:50520600-50525800	Strong transcription	Brain Cingulate Gyrus	brain
31	chr12:50520600-50525800	Strong transcription	Colonic Mucosa	Colon
32	chr12:50520600-50525800	Strong transcription	HMEC	breast
33	chr12:50520600-50526400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:50520600-50526600	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr12:50520600-50526600	Strong transcription	Osteobl	bone
36	chr12:50520600-50528400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:50520600-50528400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:50520600-50528800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:50520600-50533800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr12:50520600-50537400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:50520600-50537800	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:50520600-50537800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:50520600-50538000	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr12:50520600-50538200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:50520600-50538200	Strong transcription	Fetal Thymus	thymus
46	chr12:50520600-50538400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:50520600-50538600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:50520600-50538600	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:50520800-50525000	Strong transcription	NH-A	brain
50	chr12:50520800-50525200	Strong transcription	Brain Hippocampus Middle	brain

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