Variant report

Variant	rs2277355
Chromosome Location	chr12:50537060-50537061
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50529645..50533801-chr12:50534954..50538460,5	MCF-7	breast:
2	chr12:50467353..50469226-chr12:50536812..50539286,2	MCF-7	breast:
3	chr12:50525700..50528015-chr12:50536583..50539181,2	MCF-7	breast:
4	chr12:50478449..50481902-chr12:50536030..50539935,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066117	Chromatin interaction
ENSG00000139624	Chromatin interaction
ENSG00000110881	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10735822	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10735823	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10747571	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783336	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10783337	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10783339	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10783341	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10875999	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10876001	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876002	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876004	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10876006	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10876007	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169283	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169284	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169285	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12229758	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12314572	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17124448	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1862044	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs2008537	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2242507	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3782323	0.89[GIH][hapmap]
rs55639096	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56151073	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7131794	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7139363	0.89[GIH][hapmap]
rs7297864	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7300549	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs7305558	0.89[GIH][hapmap]
rs7306213	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73106145	0.81[EUR][1000 genomes]
rs7314598	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7316344	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7486874	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7953174	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2277355	MCRS1	cis	parietal	SCAN
rs2277355	SMARCD1	cis	cerebellum	SCAN

Chromatin state (count:122 , 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	chr12:50511200-50538200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:50511400-50538600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:50512600-50538200	Strong transcription	Primary B cells from cord blood	blood
6	chr12:50517600-50548000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:50519200-50538200	Strong transcription	Fetal Muscle Leg	muscle
8	chr12:50519400-50538400	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:50519600-50537800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:50519600-50538200	Strong transcription	Fetal Muscle Trunk	muscle
11	chr12:50520200-50537800	Strong transcription	Primary T cells from cord blood	blood
12	chr12:50520200-50539000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:50520400-50538000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:50520600-50537400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:50520600-50537800	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:50520600-50537800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:50520600-50538000	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr12:50520600-50538200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:50520600-50538200	Strong transcription	Fetal Thymus	thymus
20	chr12:50520600-50538400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:50520600-50538600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:50520600-50538600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:50520800-50537800	Strong transcription	Fetal Lung	lung
24	chr12:50520800-50538200	Strong transcription	Thymus	Thymus
25	chr12:50521200-50538400	Strong transcription	HSMMtube	muscle
26	chr12:50521400-50537200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:50521600-50538400	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr12:50522800-50538200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:50522800-50538400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:50522800-50538600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:50523000-50537200	Strong transcription	Fetal Brain Female	brain
32	chr12:50523400-50538600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:50523600-50537800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:50523600-50537800	Strong transcription	HepG2	liver
35	chr12:50523800-50537600	Strong transcription	Primary B cells from peripheral blood	blood
36	chr12:50523800-50538400	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr12:50524000-50538600	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr12:50524000-50559800	Weak transcription	Right Atrium	heart
39	chr12:50524600-50541600	Weak transcription	Psoas Muscle	Psoas
40	chr12:50527400-50538200	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr12:50528600-50537200	Weak transcription	Pancreas	Pancrea
42	chr12:50528800-50538000	Weak transcription	Hela-S3	cervix
43	chr12:50528800-50543000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr12:50529200-50538200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:50529200-50538400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:50529400-50537800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:50529400-50538000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:50529600-50537800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:50529600-50538200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:50529600-50542800	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links