Variant report

Variant	rs705700
Chromosome Location	chr12:56389293-56389294
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:26)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HNF4A	chr12:56389191-56389530	HepG2	liver:	n/a	chr12:56389343-56389357
2	CTCF	chr12:56389180-56389330	NHDF-neo	bronchial:	n/a	n/a
3	HNF4A	chr12:56389213-56389497	HepG2	liver:	n/a	chr12:56389343-56389357

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56384934..56392097-chr12:56507991..56512680,9	MCF-7	breast:
2	chr12:56365739..56372949-chr12:56384756..56392202,12	MCF-7	breast:
3	chr12:56360624..56364064-chr12:56389013..56391447,3	K562	blood:
4	chr12:56352386..56354145-chr12:56388727..56390265,2	MCF-7	breast:
5	chr12:56388983..56390811-chr12:56431023..56433319,3	K562	blood:
6	chr12:56388663..56390972-chr12:56509029..56512021,2	K562	blood:
7	chr12:56387597..56389649-chr12:56389907..56392542,2	MCF-7	breast:
8	chr12:56386715..56395273-chr12:56398367..56404356,15	MCF-7	breast:
9	chr12:56380547..56382157-chr12:56387851..56389838,2	MCF-7	breast:
10	chr12:56386022..56392601-chr12:56434180..56439537,11	MCF-7	breast:
11	chr12:56388556..56391684-chr12:56495441..56499573,3	K562	blood:
12	chr12:54346604..54348819-chr12:56388930..56391042,2	MCF-7	breast:
13	chr12:56121261..56123274-chr12:56389263..56391155,2	K562	blood:
14	chr12:56387772..56393921-chr12:56435042..56439277,13	MCF-7	breast:
15	chr12:56383457..56387356-chr12:56388448..56393059,5	MCF-7	breast:
16	chr12:56366407..56369311-chr12:56387983..56390869,4	K562	blood:
17	chr12:56209991..56213836-chr12:56388557..56392258,6	MCF-7	breast:
18	chr12:56386929..56389419-chr7:45023061..45025903,2	MCF-7	breast:
19	chr12:56387978..56391684-chr12:56496583..56499573,3	K562	blood:
20	chr12:56319711..56323865-chr12:56387409..56394085,7	MCF-7	breast:
21	chr12:56388289..56393996-chr12:56394860..56404076,14	K562	blood:
22	chr12:56388988..56394527-chr12:56433794..56442585,20	K562	blood:
23	chr12:56389168..56393063-chr12:56410604..56414258,3	K562	blood:
24	chr12:56387786..56391013-chr12:56472110..56474187,3	MCF-7	breast:
25	chr12:56382621..56386738-chr12:56387166..56390175,5	K562	blood:
26	chr12:56367522..56369913-chr12:56387381..56390070,3	MCF-7	breast:

No data

Variant related genes	Relation type
SUOX	TF binding region
ENSG00000258554	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000123407	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000255990	Chromatin interaction
ENSG00000232956	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000111540	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1081975	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10876864	0.92[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs1131017	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs11550558	0.81[LWK][hapmap]
rs1701704	0.82[JPT][hapmap]
rs1873914	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2048036	0.91[ASN][1000 genomes]
rs2069408	0.89[CHB][hapmap]
rs2456973	0.82[JPT][hapmap]
rs61937247	0.91[ASN][1000 genomes]
rs61937248	0.91[ASN][1000 genomes]
rs61937249	0.91[ASN][1000 genomes]
rs705698	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs705699	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs705702	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs705704	0.82[JPT][hapmap]
rs772920	0.90[ASN][1000 genomes]
rs772921	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs773108	0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs773109	0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs773110	0.90[ASN][1000 genomes]
rs773111	0.90[ASN][1000 genomes]
rs773112	0.89[ASN][1000 genomes]
rs773114	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs773125	0.82[AMR][1000 genomes];0.87[EUR][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:24)

SNP	Gene	Cis/trans	Tissue	Source
rs705700	SUOX	cis	lung	GTEx
rs705700	RPS26	cis	lymphoblastoid	seeQTL
rs705700	AC034102.1	cis	Muscle Skeletal	GTEx
rs705700	SUOX	cis	Nerve Tibial	GTEx
rs705700	SUOX	cis	Artery Tibial	GTEx
rs705700	ACVR1B	cis	parietal	SCAN
rs705700	SUOX	cis	Artery Aorta	GTEx
rs705700	DEFB124	trans	lymphoblastoid	RTeQTL
rs705700	SUOX	cis	Thyroid	GTEx
rs705700	FLT1	trans	lymphoblastoid	seeQTL
rs705700	SUOX	cis	cerebellum	SCAN
rs705700	SUOX	cis	Skin Sun Exposed Lower leg	GTEx
rs705700	INHBC	cis	cerebellum	SCAN
rs705700	RPS26P11	trans	lymphoblastoid	seeQTL
rs705700	HOXC8	cis	cerebellum	SCAN
rs705700	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs705700	DNAJC14	cis	parietal	SCAN
rs705700	SUOX	cis	parietal	SCAN
rs705700	CSRNP2	cis	parietal	SCAN
rs705700	SUOX	cis	Esophagus Muscularis	GTEx
rs705700	ERBB3	cis	parietal	SCAN
rs705700	RPS26	cis	multi-tissue	Pritchard
rs705700	RAB5B	cis	Muscle Skeletal	GTEx
rs705700	COQ10A	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56369400-56389400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:56369800-56389600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:56370000-56389600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:56370000-56389600	Strong transcription	Fetal Thymus	thymus
5	chr12:56370200-56389600	Strong transcription	Fetal Muscle Trunk	muscle
6	chr12:56370600-56389600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:56371400-56389600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr12:56372400-56390000	Strong transcription	Placenta	Placenta
9	chr12:56372800-56389400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:56372800-56389600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:56372800-56389600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:56373400-56389400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:56373400-56389600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:56374000-56389600	Strong transcription	Fetal Stomach	stomach
15	chr12:56375800-56390600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:56376000-56389600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:56376600-56389600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:56377000-56389400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:56377400-56389400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr12:56377600-56389600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:56377800-56389600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:56378000-56389600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:56378200-56389600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:56378400-56389400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr12:56378400-56389400	Strong transcription	Primary B cells from peripheral blood	blood
26	chr12:56378400-56389600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:56378600-56389400	Strong transcription	Brain Cingulate Gyrus	brain
28	chr12:56378800-56389400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr12:56379000-56389400	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:56379000-56389600	Strong transcription	Brain Hippocampus Middle	brain
31	chr12:56379000-56389600	Strong transcription	HSMMtube	muscle
32	chr12:56379000-56389600	Strong transcription	NH-A	brain
33	chr12:56379800-56389400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr12:56379800-56389400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr12:56380200-56389400	Strong transcription	Fetal Brain Female	brain
36	chr12:56380600-56389600	Strong transcription	Fetal Muscle Leg	muscle
37	chr12:56382000-56389400	Strong transcription	Osteobl	bone
38	chr12:56383400-56389600	Strong transcription	HSMM	muscle
39	chr12:56385000-56389600	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr12:56385200-56390200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr12:56385200-56390600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr12:56385400-56390200	Weak transcription	Fetal Heart	heart
43	chr12:56385600-56390200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr12:56386200-56389600	Genic enhancers	Fetal Intestine Large	intestine
45	chr12:56386200-56390200	Weak transcription	Stomach Mucosa	stomach
46	chr12:56386400-56389600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:56387400-56390400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr12:56387600-56390200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr12:56387600-56390200	Weak transcription	Brain Substantia Nigra	brain
50	chr12:56387800-56390200	Weak transcription	A549	lung

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