Variant report

Variant	rs2339398
Chromosome Location	chr1:152843098-152843099
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:152717585..152718578-chr1:152842088..152843110,3	MCF-7	breast:
2	chr1:152842063..152844434-chr1:153164775..153166274,11	MCF-7	breast:
3	chr1:152626130..152627645-chr1:152842015..152844012,15	MCF-7	breast:
4	chr1:152843080..152844798-chr1:153164828..153166213,18	MCF-7	breast:
5	chr1:152841405..152843459-chr1:152858865..152861299,2	K562	blood:
6	chr1:152715224..152717554-chr1:152841619..152843723,2	MCF-7	breast:
7	chr1:152841334..152844015-chr1:152851385..152853978,2	K562	blood:

Variant related genes	Relation type
ENSG00000233819	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10494280	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11205126	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11205127	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11205128	0.85[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11205129	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs11801996	1.00[CEU][hapmap];0.82[CHD][hapmap];0.92[MEX][hapmap];1.00[EUR][1000 genomes]
rs12021601	0.82[CHD][hapmap];0.92[MEX][hapmap]
rs12022349	1.00[CEU][hapmap]
rs12026193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12048655	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12239814	0.84[MEX][hapmap]
rs12568299	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16834715	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2339396	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2339397	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2879485	0.84[MEX][hapmap]
rs3737862	0.82[CHD][hapmap];0.92[MEX][hapmap]
rs4240862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4240863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4363387	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4845325	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs4845489	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845494	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs58021079	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61482767	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6659798	0.91[CHB][hapmap];0.91[CHD][hapmap]
rs73006590	1.00[EUR][1000 genomes]
rs7552416	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs7553755	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7556490	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv427786	chr1:152572990-152898153	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv999918	chr1:152749733-152861866	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1009885	chr1:152762750-152851273	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1000159	chr1:152809514-152853766	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1008447	chr1:152811171-152853748	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv2761937	chr1:152811183-152853760	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv831592	chr1:152815054-152997162	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2339398	S100A6	cis	lymphoblastoid	seeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152838800-152846000	Weak transcription	HMEC	breast
2	chr1:152839200-152843800	Weak transcription	NHEK	skin
3	chr1:152840600-152843600	Weak transcription	Fetal Stomach	stomach
4	chr1:152842800-152843200	Weak transcription	GM12878-XiMat	blood

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