Variant report

Variant	rs10779415
Chromosome Location	chr1:220935808-220935809
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:220935174..220937582-chr1:220941200..220942748,2	MCF-7	breast:
2	chr1:220934709..220937356-chr1:220938309..220941059,2	K562	blood:
3	chr1:220933592..220936563-chr1:220940646..220943203,2	MCF-7	breast:
4	chr1:220921708..220923550-chr1:220934385..220936474,2	MCF-7	breast:
5	chr1:220935678..220937242-chr1:220938232..220939996,2	MCF-7	breast:
6	chr1:220926792..220928893-chr1:220934076..220936520,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117791	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10863562	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11118597	1.00[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11118599	0.83[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11118600	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs11809755	0.92[AMR][1000 genomes]
rs12027850	0.83[CEU][hapmap]
rs12402066	0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12562235	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12568838	0.83[CEU][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12738691	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12758783	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17008609	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs17008613	0.81[CEU][hapmap];0.81[MEX][hapmap];0.84[EUR][1000 genomes]
rs234223	0.82[EUR][1000 genomes]
rs2642424	0.83[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap]
rs2935225	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2994529	0.86[EUR][1000 genomes]
rs2994530	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3015251	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3015252	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs337147	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs337148	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs337150	0.91[EUR][1000 genomes]
rs337164	0.86[EUR][1000 genomes]
rs337187	0.84[EUR][1000 genomes]
rs337189	0.93[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs337190	0.93[CEU][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs337191	0.88[EUR][1000 genomes]
rs365346	0.87[CEU][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs365398	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs365693	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3753878	0.91[AMR][1000 genomes]
rs3795536	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381023	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs382959	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs386118	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs391315	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs393585	0.93[CEU][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs4131748	0.81[CEU][hapmap]
rs421736	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs425473	1.00[CEU][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs439130	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs443071	0.93[CEU][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs443189	0.92[EUR][1000 genomes]
rs6657944	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs6659246	0.86[LWK][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes]
rs6659604	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6697965	0.83[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7518916	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7519399	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7519414	0.83[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7536276	0.82[CEU][hapmap]
rs7539769	0.83[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7542648	0.83[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7542723	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7553948	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7556458	0.83[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7556561	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs774138	0.86[EUR][1000 genomes]
rs9430990	1.00[CEU][hapmap]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10779415	MOSC2	cis	cerebellum	SCAN
rs10779415	C1orf115	cis	lymphoblastoid	seeQTL
rs10779415	MOSC2	cis	lymphoblastoid	seeQTL
rs10779415	MOSC2	Cis_1M	lymphoblastoid	RTeQTL
rs10779415	C1orf115	Cis_1M	lymphoblastoid	RTeQTL
rs10779415	IARS2	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220922600-220943800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:220922600-220946400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:220922800-220959600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:220922800-220959600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:220923200-220948000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:220924200-220936000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr1:220924600-220936800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:220924600-220944000	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:220924800-220945600	Weak transcription	Osteobl	bone
10	chr1:220925000-220946000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:220925000-220959400	Weak transcription	Brain Angular Gyrus	brain
12	chr1:220925200-220942000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:220925200-220943400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:220925400-220950200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:220925800-220938400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:220927800-220938600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:220929400-220940600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr1:220929600-220943000	Weak transcription	Brain Germinal Matrix	brain
19	chr1:220929800-220940800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:220930000-220940600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:220930000-220942400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:220930000-220943400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:220930000-220946000	Weak transcription	Fetal Brain Female	brain
24	chr1:220930000-220950000	Weak transcription	Fetal Brain Male	brain
25	chr1:220930000-220950200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:220930000-220950400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:220930000-220959600	Weak transcription	Psoas Muscle	Psoas
28	chr1:220930200-220936200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:220930200-220937800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:220930200-220940800	Weak transcription	NHLF	lung
31	chr1:220930200-220944000	Weak transcription	Colon Smooth Muscle	Colon
32	chr1:220930200-220950000	Weak transcription	Brain Anterior Caudate	brain
33	chr1:220930400-220950000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:220930400-220959600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:220930600-220950000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:220930800-220946000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:220931000-220946200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:220931200-220940400	Weak transcription	Fetal Kidney	kidney
39	chr1:220931200-220942400	Weak transcription	Hela-S3	cervix
40	chr1:220931200-220946600	Weak transcription	HUVEC	blood vessel
41	chr1:220931200-220959000	Weak transcription	Brain Substantia Nigra	brain
42	chr1:220931400-220944400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr1:220932800-220937000	Strong transcription	Aorta	Aorta
44	chr1:220932800-220939400	Strong transcription	Fetal Muscle Leg	muscle
45	chr1:220933400-220936000	Enhancers	Liver	Liver
46	chr1:220934400-220938400	Strong transcription	Left Ventricle	heart
47	chr1:220934400-220939000	Genic enhancers	Fetal Intestine Small	intestine
48	chr1:220934600-220936000	Enhancers	HepG2	liver
49	chr1:220934600-220936600	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr1:220934600-220936600	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links