Variant report

Variant	rs773111
Chromosome Location	chr12:56375740-56375741
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr12:56375704-56376052	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr12:56375698-56376008	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr12:56375725-56375914	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr12:56375698-56376001	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr12:56375695-56376000	MCF10A-Er-Src	breast:	n/a	n/a
6	EGR1	chr12:56375717-56375943	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56222612..56225517-chr12:56372520..56376647,5	MCF-7	breast:
2	chr12:56320862..56327055-chr12:56370927..56377943,9	MCF-7	breast:
3	chr12:56375142..56377081-chr12:56377358..56380445,4	MCF-7	breast:
4	chr12:56350213..56352992-chr12:56373952..56376823,2	MCF-7	breast:
5	chr12:56375563..56379260-chr12:56388752..56391429,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237493	TF binding region
ENSG00000065357	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000139531	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1081975	0.83[ASN][1000 genomes]
rs1689510	0.83[EUR][1000 genomes]
rs1873914	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2048036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61937247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61937248	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61937249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs705698	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs705699	0.91[ASN][1000 genomes]
rs705700	0.90[ASN][1000 genomes]
rs705702	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs772920	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs772921	0.82[EUR][1000 genomes]
rs773107	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs773108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773109	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs773110	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773112	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs773114	0.93[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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs773111	SUOX	cis	Nerve Tibial	GTEx
rs773111	SUOX	cis	lung	GTEx
rs773111	DEFB124	trans	lymphoblastoid	RTeQTL
rs773111	RPS26	cis	multi-tissue	Pritchard
rs773111	RAB5B	cis	Muscle Skeletal	GTEx
rs773111	SUOX	cis	Thyroid	GTEx
rs773111	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs773111	AC034102.1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56368600-56383200	Weak transcription	Gastric	stomach
2	chr12:56368800-56379000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:56369000-56383600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:56369200-56376200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:56369200-56376200	Weak transcription	NHDF-Ad	bronchial
6	chr12:56369200-56379000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:56369200-56380000	Weak transcription	Right Ventricle	heart
8	chr12:56369200-56380400	Weak transcription	Aorta	Aorta
9	chr12:56369200-56383600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:56369200-56384600	Weak transcription	Psoas Muscle	Psoas
11	chr12:56369400-56379400	Strong transcription	Fetal Muscle Leg	muscle
12	chr12:56369400-56381000	Weak transcription	Small Intestine	intestine
13	chr12:56369400-56383400	Weak transcription	Pancreas	Pancrea
14	chr12:56369400-56384200	Weak transcription	Fetal Brain Male	brain
15	chr12:56369400-56389400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:56369800-56389600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:56370000-56376400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:56370000-56389600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:56370000-56389600	Strong transcription	Fetal Thymus	thymus
20	chr12:56370200-56389600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr12:56370400-56385000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:56370400-56388400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:56370600-56376200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:56370600-56376400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:56370600-56379000	Weak transcription	Brain Hippocampus Middle	brain
26	chr12:56370600-56383200	Weak transcription	HepG2	liver
27	chr12:56370600-56383400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr12:56370600-56388200	Strong transcription	Dnd41	blood
29	chr12:56370600-56389600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:56370800-56376600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr12:56370800-56378600	Weak transcription	Brain Substantia Nigra	brain
32	chr12:56370800-56383400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr12:56371000-56377600	Weak transcription	Left Ventricle	heart
34	chr12:56371000-56379600	Weak transcription	Right Atrium	heart
35	chr12:56371400-56375800	Strong transcription	NHLF	lung
36	chr12:56371400-56381800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr12:56371400-56389600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:56371600-56376200	Weak transcription	Fetal Heart	heart
39	chr12:56371600-56383400	Weak transcription	Colon Smooth Muscle	Colon
40	chr12:56371600-56388800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:56371800-56375800	Weak transcription	Primary T cells from cord blood	blood
42	chr12:56371800-56376200	Weak transcription	K562	blood
43	chr12:56371800-56383400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr12:56372000-56378000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr12:56372000-56380800	Weak transcription	Ovary	ovary
46	chr12:56372400-56376600	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr12:56372400-56379600	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr12:56372400-56390000	Strong transcription	Placenta	Placenta
49	chr12:56372600-56377000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:56372800-56376000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links