Variant report

Variant	rs773109
Chromosome Location	chr12:56374695-56374696
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr12:56350213..56352992-chr12:56373952..56376823,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000065357	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000170473	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1081975	0.82[ASN][1000 genomes]
rs10876864	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs10876870	0.82[JPT][hapmap]
rs11171739	0.82[JPT][hapmap]
rs1131017	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs1689510	0.83[EUR][1000 genomes]
rs1701704	0.91[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap]
rs1873914	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2048036	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2069408	0.95[CHB][hapmap];0.82[YRI][hapmap]
rs2069415	1.00[YRI][hapmap]
rs2271194	0.83[JPT][hapmap]
rs2456973	0.91[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap]
rs3741499	0.82[JPT][hapmap]
rs4759229	0.82[JPT][hapmap]
rs61937247	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61937248	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61937249	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs705698	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs705699	1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs705700	0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs705702	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs705704	0.91[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap]
rs772920	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs772921	0.91[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs773107	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs773108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];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];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs773111	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs773112	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs773114	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs7971751	0.82[JPT][hapmap]
rs877636	0.82[JPT][hapmap]

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	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
4	nsv973073	chr12:56373818-56374702	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs773109	SUOX	cis	lung	GTEx
rs773109	RAB5B	cis	Muscle Skeletal	GTEx
rs773109	RPS26///RPS26L///LOC644166///LOC644191	cis	lesional skin	skin_eQTL
rs773109	RPS26	cis	multi-tissue	Pritchard
rs773109	RPS26///RPS26L///LOC644166///LOC644191	cis	uninvolved skin	skin_eQTL
rs773109	DEFB124	trans	lymphoblastoid	RTeQTL
rs773109	SUOX	cis	Nerve Tibial	GTEx
rs773109	AC034102.1	cis	Muscle Skeletal	GTEx
rs773109	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs773109	SUOX	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56368600-56375400	Weak transcription	Lung	lung
2	chr12:56368600-56383200	Weak transcription	Gastric	stomach
3	chr12:56368800-56379000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:56369000-56383600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:56369200-56375000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:56369200-56375200	Weak transcription	A549	lung
7	chr12:56369200-56376200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:56369200-56376200	Weak transcription	NHDF-Ad	bronchial
9	chr12:56369200-56379000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:56369200-56380000	Weak transcription	Right Ventricle	heart
11	chr12:56369200-56380400	Weak transcription	Aorta	Aorta
12	chr12:56369200-56383600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr12:56369200-56384600	Weak transcription	Psoas Muscle	Psoas
14	chr12:56369400-56375200	Weak transcription	Fetal Brain Female	brain
15	chr12:56369400-56375200	Weak transcription	Fetal Kidney	kidney
16	chr12:56369400-56379400	Strong transcription	Fetal Muscle Leg	muscle
17	chr12:56369400-56381000	Weak transcription	Small Intestine	intestine
18	chr12:56369400-56383400	Weak transcription	Pancreas	Pancrea
19	chr12:56369400-56384200	Weak transcription	Fetal Brain Male	brain
20	chr12:56369400-56389400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:56369800-56389600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:56370000-56375200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:56370000-56376400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:56370000-56389600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:56370000-56389600	Strong transcription	Fetal Thymus	thymus
26	chr12:56370200-56375400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:56370200-56375400	Strong transcription	NHEK	skin
28	chr12:56370200-56389600	Strong transcription	Fetal Muscle Trunk	muscle
29	chr12:56370400-56375000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:56370400-56385000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr12:56370400-56388400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:56370600-56375600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:56370600-56376200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr12:56370600-56376400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:56370600-56379000	Weak transcription	Brain Hippocampus Middle	brain
36	chr12:56370600-56383200	Weak transcription	HepG2	liver
37	chr12:56370600-56383400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:56370600-56388200	Strong transcription	Dnd41	blood
39	chr12:56370600-56389600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:56370800-56375200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:56370800-56376600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:56370800-56378600	Weak transcription	Brain Substantia Nigra	brain
43	chr12:56370800-56383400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr12:56371000-56377600	Weak transcription	Left Ventricle	heart
45	chr12:56371000-56379600	Weak transcription	Right Atrium	heart
46	chr12:56371200-56375600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:56371400-56375800	Strong transcription	NHLF	lung
48	chr12:56371400-56381800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr12:56371400-56389600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:56371600-56375200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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