Variant report

Variant	rs1953399
Chromosome Location	chr14:70223570-70223571
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:70221981..70224233-chr14:70227163..70228798,2	K562	blood:
2	chr14:70219020..70221233-chr14:70223129..70224904,2	MCF-7	breast:
3	chr14:70218805..70221409-chr14:70223548..70226487,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10130926	0.92[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10136397	0.89[EUR][1000 genomes]
rs10142027	0.88[ASN][1000 genomes]
rs10142031	0.88[ASN][1000 genomes]
rs10142686	0.87[ASN][1000 genomes]
rs10143223	0.81[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs10146537	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10148404	0.89[EUR][1000 genomes]
rs10151895	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10459536	0.95[ASN][1000 genomes]
rs11620808	0.92[CEU][hapmap];0.81[CHB][hapmap];0.89[EUR][1000 genomes]
rs11621916	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11622580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11622925	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11623262	0.92[EUR][1000 genomes]
rs11624523	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11624532	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11625731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11625932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11627012	0.92[EUR][1000 genomes]
rs11627089	0.89[EUR][1000 genomes]
rs11628423	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11628546	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs11628665	0.91[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs11629054	1.00[CHD][hapmap]
rs12431573	0.80[CHD][hapmap];0.82[ASN][1000 genomes]
rs13313365	0.89[EUR][1000 genomes]
rs13313366	0.89[EUR][1000 genomes]
rs14411	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs17328	0.80[CHD][hapmap];0.82[ASN][1000 genomes]
rs1953400	0.96[ASN][1000 genomes]
rs2148503	0.95[ASN][1000 genomes]
rs2148505	0.93[ASN][1000 genomes]
rs2332167	0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs28404963	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28437671	0.89[EUR][1000 genomes]
rs28437822	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28480224	0.85[EUR][1000 genomes]
rs2877595	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28785205	0.92[EUR][1000 genomes]
rs28847646	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3104	0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs3784152	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3784153	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3809399	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4646285	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4646286	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs4646297	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4899311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4899313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902752	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902753	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902755	0.95[ASN][1000 genomes]
rs55724465	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55987626	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56074637	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56140822	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56177148	0.89[EUR][1000 genomes]
rs57492222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58582364	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59066042	0.89[EUR][1000 genomes]
rs59172911	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60442313	0.95[ASN][1000 genomes]
rs61356864	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6573905	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6573906	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6573907	0.94[ASN][1000 genomes]
rs6573908	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7142868	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7153496	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7153985	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7154439	0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[ASN][1000 genomes]
rs7160953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7161476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72725718	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72725724	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72725740	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72725743	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72725745	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72725776	0.82[EUR][1000 genomes]
rs72725780	0.82[EUR][1000 genomes]
rs8010836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8011311	0.91[ASN][1000 genomes]
rs8013598	0.91[ASN][1000 genomes]
rs8014236	0.89[ASN][1000 genomes]
rs8021735	0.82[ASN][1000 genomes]
rs9944036	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[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	nsv456336	chr14:70081956-70574149	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv565007	chr14:70081956-70574149	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1953399	PSMC3	trans	cerebellum	SCAN
rs1953399	TTC9	cis	parietal	SCAN
rs1953399	SLC8A3	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70220800-70223600	Enhancers	Fetal Intestine Large	intestine
2	chr14:70221000-70223600	Enhancers	Fetal Intestine Small	intestine
3	chr14:70221000-70227200	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr14:70222400-70233000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr14:70222600-70227400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr14:70223000-70228800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr14:70223200-70228400	Weak transcription	Primary T cells from cord blood	blood
8	chr14:70223200-70232400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr14:70223400-70224400	Weak transcription	HepG2	liver
10	chr14:70223400-70224400	Weak transcription	K562	blood
11	chr14:70223400-70228800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr14:70223400-70232400	Weak transcription	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links