Variant report

Variant	rs579518
Chromosome Location	chr7:140777030-140777031
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:140776160..140778796-chr7:140827028..140829508,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10215245	0.82[ASN][1000 genomes]
rs1044927	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1089264	0.86[ASN][1000 genomes]
rs10952364	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12703284	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13234490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13236704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1476816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1533933	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17630683	0.80[ASN][1000 genomes]
rs1860720	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1961288	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2079978	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2688430	0.86[ASN][1000 genomes]
rs3805116	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs38715	1.00[CHB][hapmap]
rs38720	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs38722	1.00[CHB][hapmap]
rs38723	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs38726	0.85[CHB][hapmap]
rs38734	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs38736	0.82[ASN][1000 genomes]
rs38739	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs38740	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4726225	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs488795	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs490810	0.95[ASN][1000 genomes]
rs512177	1.00[ASN][1000 genomes]
rs512509	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs528957	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs533441	1.00[ASN][1000 genomes]
rs544081	0.98[ASN][1000 genomes]
rs545121	1.00[ASN][1000 genomes]
rs557962	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs55971084	0.82[ASN][1000 genomes]
rs569584	0.98[ASN][1000 genomes]
rs6464217	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6464260	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6464284	0.95[ASN][1000 genomes]
rs6662	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs6967214	0.89[ASN][1000 genomes]
rs6971577	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7792447	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7801518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs801117	0.86[ASN][1000 genomes]
rs801121	0.86[ASN][1000 genomes]
rs801127	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs801155	0.98[ASN][1000 genomes]
rs801159	1.00[ASN][1000 genomes]
rs9274	1.00[CHB][hapmap]

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	nsv889248	chr7:140754785-140809205	Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3417140	chr7:140768130-140783190	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs579518	IFI16	trans	cerebellum	SCAN
rs579518	YIPF5	trans	cerebellum	SCAN
rs579518	MRPS33	Cis_1M	lymphoblastoid	RTeQTL
rs579518	ADCK2	cis	cerebellum	SCAN
rs579518	HIPK2	cis	parietal	SCAN
rs579518	CLEC5A	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140774800-140783200	Weak transcription	Pancreas	Pancrea
2	chr7:140776000-140778600	Active TSS	Brain Anterior Caudate	brain
3	chr7:140776600-140777200	Flanking Active TSS	Brain Germinal Matrix	brain
4	chr7:140776800-140778400	Weak transcription	Psoas Muscle	Psoas
5	chr7:140776800-140782800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:140776800-140783200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr7:140776800-140783200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr7:140776800-140783200	Weak transcription	Brain Angular Gyrus	brain
9	chr7:140776800-140783200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr7:140776800-140783200	Weak transcription	Fetal Brain Male	brain
11	chr7:140777000-140777200	Weak transcription	Fetal Brain Female	brain
12	chr7:140777000-140777200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr7:140777000-140778000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr7:140777000-140785000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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