Variant report

Variant	rs6543459
Chromosome Location	chr2:98894287-98894288
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10172281	0.82[AFR][1000 genomes]
rs10176056	1.00[ASN][1000 genomes]
rs10181000	0.80[CEU][hapmap];0.82[CHB][hapmap];0.84[AFR][1000 genomes]
rs10190336	0.84[ASN][1000 genomes]
rs10199476	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs10201994	0.98[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10202618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10203437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11124096	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[YRI][hapmap]
rs11124107	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11124121	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11673807	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap]
rs11679920	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap]
rs11889349	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11891512	0.82[ASN][1000 genomes]
rs11895654	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs11901562	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12470615	0.92[YRI][hapmap]
rs12478763	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12478769	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12622324	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs12624294	1.00[ASN][1000 genomes]
rs12712256	0.92[ASN][1000 genomes]
rs12993718	0.82[ASN][1000 genomes]
rs12999985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap]
rs13013876	0.82[ASN][1000 genomes]
rs13014142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap]
rs13033263	0.82[ASN][1000 genomes]
rs13394706	0.82[CHB][hapmap]
rs13415414	1.00[ASN][1000 genomes]
rs13428221	0.83[ASN][1000 genomes]
rs1451251	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs1466944	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs1504679	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17427684	0.98[ASN][1000 genomes]
rs17428056	1.00[ASN][1000 genomes]
rs17429208	0.87[CHB][hapmap]
rs17493655	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17493788	1.00[ASN][1000 genomes]
rs1875880	0.98[ASN][1000 genomes]
rs2102270	0.87[CHB][hapmap]
rs2122756	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2202387	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2221416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2292118	0.80[CEU][hapmap];0.88[CHB][hapmap];0.85[AFR][1000 genomes]
rs2292119	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs3731659	0.98[ASN][1000 genomes]
rs4374424	1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[YRI][hapmap];0.82[ASN][1000 genomes]
rs4389366	0.92[ASN][1000 genomes]
rs4455212	1.00[CHB][hapmap];0.92[YRI][hapmap]
rs4477970	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4479470	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4494805	0.82[ASN][1000 genomes]
rs4535095	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4608580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4632400	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4851122	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4851123	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851124	0.98[ASN][1000 genomes]
rs4851935	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap]
rs4851951	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs4851952	0.82[ASN][1000 genomes]
rs4851954	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4851955	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851959	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851960	0.91[ASN][1000 genomes]
rs62157914	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6543419	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs66464436	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715989	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6725543	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6742930	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6747344	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap]
rs6747410	0.87[CHB][hapmap]
rs6750975	0.98[ASN][1000 genomes]
rs6754222	0.80[CEU][hapmap];0.82[CHB][hapmap];0.84[AFR][1000 genomes]
rs72933220	1.00[ASN][1000 genomes]
rs7572757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7574218	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7578802	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.82[ASN][1000 genomes]
rs7586663	0.81[AFR][1000 genomes]
rs7589018	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598554	0.92[ASN][1000 genomes]
rs7601049	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap]
rs7606070	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7606220	1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[YRI][hapmap]
rs937726	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1004082	chr2:98792256-98967681	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535833	chr2:98792256-98967681	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1002366	chr2:98877050-98904494	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98888800-98897000	Weak transcription	Ovary	ovary
2	chr2:98893600-98894400	Enhancers	Fetal Kidney	kidney
3	chr2:98893600-98895600	Enhancers	Placenta	Placenta
4	chr2:98893600-98897000	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr2:98893800-98894800	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr2:98894000-98896800	Enhancers	Stomach Mucosa	stomach
7	chr2:98894000-98897400	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr2:98894200-98895800	Weak transcription	Duodenum Mucosa	Duodenum

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