Variant report

Variant	rs7972842
Chromosome Location	chr12:50516323-50516324
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50513121..50517277-chr12:50517671..50521204,4	MCF-7	breast:
2	chr12:50515617..50517126-chr12:50524632..50526499,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1044370	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10747570	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169294	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11831413	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12815871	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12824125	0.86[EUR][1000 genomes]
rs12830386	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1862043	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2178173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2358538	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34573394	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35549836	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35998534	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56709084	0.86[ASN][1000 genomes]
rs646782	1.00[CHB][hapmap]
rs6580729	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66768395	0.81[ASN][1000 genomes]
rs706791	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs706792	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs706793	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7136570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294548	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7297421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301649	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7301740	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7308356	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7532	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967705	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7967844	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs836170	0.86[ASN][1000 genomes]
rs836171	0.88[ASN][1000 genomes]
rs836172	1.00[CHB][hapmap];1.00[JPT][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];1.00[JPT][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];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs836180	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs836181	0.80[ASN][1000 genomes]
rs860698	1.00[CHB][hapmap];1.00[JPT][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7972842	CERS5	cis	Nerve Tibial	GTEx
rs7972842	LASS5	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50506800-50521000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:50506800-50523600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:50507000-50520800	Weak transcription	Fetal Lung	lung
4	chr12:50507000-50520800	Weak transcription	NH-A	brain
5	chr12:50507000-50522400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:50507000-50522800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:50507000-50522800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:50507000-50523600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:50507000-50537400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:50507000-50539600	Weak transcription	Stomach Mucosa	stomach
11	chr12:50507200-50519000	Weak transcription	HUVEC	blood vessel
12	chr12:50507200-50520800	Weak transcription	NHDF-Ad	bronchial
13	chr12:50507200-50520800	Weak transcription	NHLF	lung
14	chr12:50507200-50521400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:50507200-50522600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:50507200-50523600	Weak transcription	Right Atrium	heart
17	chr12:50507200-50532000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr12:50508400-50518200	Strong transcription	Fetal Stomach	stomach
19	chr12:50508600-50518200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:50508600-50518200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr12:50508800-50518000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:50509200-50518200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:50509200-50518400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:50509400-50518000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:50509400-50518200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:50509400-50518400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:50509400-50519600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:50509400-50521600	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr12:50509400-50522600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr12:50510000-50517800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:50510000-50518200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:50510800-50523800	Weak transcription	Psoas Muscle	Psoas
33	chr12:50510800-50528400	Strong transcription	Liver	Liver
34	chr12:50511200-50519000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr12:50511200-50538200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:50511400-50518000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr12:50511400-50518200	Strong transcription	Lung	lung
38	chr12:50511400-50538600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:50512000-50518400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:50512200-50519400	Weak transcription	Fetal Heart	heart
41	chr12:50512600-50519000	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr12:50512600-50519200	Strong transcription	Adipose Nuclei	Adipose
43	chr12:50512600-50522800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:50512600-50529200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:50512600-50538200	Strong transcription	Primary B cells from cord blood	blood
46	chr12:50512800-50518000	Strong transcription	Thymus	Thymus
47	chr12:50512800-50518200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr12:50513000-50516400	Strong transcription	Colon Smooth Muscle	Colon
49	chr12:50513000-50516400	Strong transcription	A549	lung
50	chr12:50513000-50518000	Strong transcription	Esophagus	oesophagus

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