Variant report

Variant	rs12562235
Chromosome Location	chr1:220945740-220945741
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220944994..220947101-chr1:220951123..220953562,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117791	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10779415	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10863562	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11118597	0.82[EUR][1000 genomes]
rs11118598	0.82[AFR][1000 genomes]
rs11118599	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118600	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12027850	0.84[EUR][1000 genomes]
rs12402066	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568838	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17008609	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2642424	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2935225	0.81[EUR][1000 genomes]
rs3015252	0.81[EUR][1000 genomes]
rs337147	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs337148	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs337150	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs365398	0.83[EUR][1000 genomes]
rs3795536	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs381023	0.82[EUR][1000 genomes]
rs386118	0.81[EUR][1000 genomes]
rs421736	0.84[EUR][1000 genomes]
rs425473	0.84[EUR][1000 genomes]
rs439130	0.80[EUR][1000 genomes]
rs4846662	0.89[EUR][1000 genomes]
rs6657944	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6659604	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6697965	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518916	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519399	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519414	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536276	0.83[EUR][1000 genomes]
rs7539769	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7542648	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7542723	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553948	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556458	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556561	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523389	chr1:220926844-220956012	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12562235	MOSC2	Cis_1M	lymphoblastoid	RTeQTL
rs12562235	C1orf115	cis	Nerve Tibial	GTEx
rs12562235	C1orf115	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220922600-220946400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:220922800-220959600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:220922800-220959600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:220923200-220948000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:220925000-220946000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:220925000-220959400	Weak transcription	Brain Angular Gyrus	brain
7	chr1:220925400-220950200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:220930000-220946000	Weak transcription	Fetal Brain Female	brain
9	chr1:220930000-220950000	Weak transcription	Fetal Brain Male	brain
10	chr1:220930000-220950200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:220930000-220950400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:220930000-220959600	Weak transcription	Psoas Muscle	Psoas
13	chr1:220930200-220950000	Weak transcription	Brain Anterior Caudate	brain
14	chr1:220930400-220950000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:220930400-220959600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:220930600-220950000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:220930800-220946000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:220931000-220946200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:220931200-220946600	Weak transcription	HUVEC	blood vessel
20	chr1:220931200-220959000	Weak transcription	Brain Substantia Nigra	brain
21	chr1:220936200-220959600	Weak transcription	A549	lung
22	chr1:220936600-220946000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:220936600-220958200	Weak transcription	Esophagus	oesophagus
24	chr1:220939000-220960400	Weak transcription	Small Intestine	intestine
25	chr1:220941200-220949800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:220941400-220948400	Strong transcription	Fetal Muscle Leg	muscle
27	chr1:220942200-220946800	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:220942200-220948200	Strong transcription	Fetal Stomach	stomach
29	chr1:220942400-220945800	Strong transcription	Duodenum Mucosa	Duodenum
30	chr1:220942400-220950200	Weak transcription	Right Atrium	heart
31	chr1:220942400-220950200	Weak transcription	Stomach Mucosa	stomach
32	chr1:220942600-220946400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:220942800-220946200	Strong transcription	Fetal Lung	lung
34	chr1:220942800-220948200	Strong transcription	Fetal Intestine Small	intestine
35	chr1:220942800-220948800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr1:220943000-220958400	Weak transcription	HepG2	liver
37	chr1:220943000-220959000	Strong transcription	Fetal Intestine Large	intestine
38	chr1:220944000-220947800	Weak transcription	Fetal Heart	heart
39	chr1:220944200-220945800	Weak transcription	GM12878-XiMat	blood
40	chr1:220944200-220948400	Strong transcription	Left Ventricle	heart
41	chr1:220944200-220948800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr1:220944200-220950000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr1:220944200-220950000	Weak transcription	Hela-S3	cervix
44	chr1:220944200-220950200	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr1:220944200-220956000	Weak transcription	Pancreas	Pancrea
46	chr1:220944200-220959200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:220944200-220959400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:220944200-220959400	Weak transcription	Fetal Kidney	kidney
49	chr1:220944200-220959600	Weak transcription	NHLF	lung
50	chr1:220944200-220959800	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links