Variant report

Variant	rs2301516
Chromosome Location	chr1:169494384-169494385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
2	chr1:169480439..169483097-chr1:169493507..169495167,2	MCF-7	breast:
3	chr1:169352595..169354140-chr1:169494261..169496429,2	MCF-7	breast:
4	chr1:169475721..169488506-chr1:169493331..169501885,21	MCF-7	breast:
5	chr1:169483273..169484944-chr1:169493711..169496257,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198734	Chromatin interaction
ENSG00000117479	Chromatin interaction
ENSG00000213062	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10800452	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919187	0.84[ASN][1000 genomes]
rs10919188	0.84[ASN][1000 genomes]
rs10919189	0.84[ASN][1000 genomes]
rs12024849	0.85[ASN][1000 genomes]
rs12025910	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12239964	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12405595	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1557571	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800595	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894691	1.00[AFR][1000 genomes]
rs1894693	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1894703	0.85[ASN][1000 genomes]
rs2227243	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2301519	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301520	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420134	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2420135	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3766104	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4440913	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6013	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6015	0.84[ASN][1000 genomes]
rs6018	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6024	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6027	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6033	0.84[ASN][1000 genomes]
rs6036	0.84[ASN][1000 genomes]
rs6037	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72708008	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72708013	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72708039	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs916439	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332583	0.84[ASN][1000 genomes]
rs9332601	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332609	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332614	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332629	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332639	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332641	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332646	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332654	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332659	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332661	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9332673	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9332676	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs966751	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv872533	chr1:169490401-169508576	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2301516	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169483200-169495400	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr1:169483200-169496800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:169483800-169496800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr1:169484200-169494400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:169484800-169501000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:169485400-169510600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:169486600-169494400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:169487400-169501000	Weak transcription	Right Ventricle	heart
9	chr1:169489800-169494600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:169490600-169496200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:169490800-169494600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:169490800-169496200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:169490800-169496800	Weak transcription	Pancreas	Pancrea
14	chr1:169490800-169496800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:169491200-169497000	Weak transcription	Small Intestine	intestine
16	chr1:169491600-169500800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr1:169492000-169499800	Weak transcription	Left Ventricle	heart
18	chr1:169492800-169495400	Enhancers	Hela-S3	cervix
19	chr1:169493000-169496000	Genic enhancers	Liver	Liver
20	chr1:169493600-169494800	Weak transcription	Stomach Mucosa	stomach
21	chr1:169494000-169496200	Weak transcription	Placenta	Placenta
22	chr1:169494000-169496800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:169494000-169502800	Strong transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links