Variant report

Variant	rs6741998
Chromosome Location	chr2:142258882-142258883
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:142257639..142260616-chr2:142261708..142263676,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10496884	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11674506	1.00[CEU][hapmap]
rs11675776	1.00[CEU][hapmap]
rs11685267	1.00[CEU][hapmap]
rs11690880	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12992656	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs12993733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12993821	1.00[CEU][hapmap]
rs12994255	0.88[EUR][1000 genomes]
rs13001306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13001716	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13006974	1.00[CEU][hapmap]
rs13009586	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13018345	0.82[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13023434	1.00[YRI][hapmap]
rs13030953	1.00[CEU][hapmap]
rs13393425	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1471675	1.00[CEU][hapmap]
rs16846362	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs17548023	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17552442	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17616060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17734546	1.00[CEU][hapmap]
rs17735355	1.00[CEU][hapmap]
rs17735674	1.00[CEU][hapmap]
rs17791242	1.00[CEU][hapmap]
rs17791266	1.00[CEU][hapmap]
rs17792070	1.00[CEU][hapmap]
rs1842932	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2890614	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs34050146	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34470585	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34531296	0.95[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs34571231	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35266942	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs35390851	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs36057199	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4328578	0.90[ASN][1000 genomes]
rs4340448	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4363970	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4583399	1.00[YRI][hapmap]
rs4588128	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4635467	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs60727330	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6429882	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs66741925	0.88[EUR][1000 genomes]
rs6717454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6744016	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6746208	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6748629	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6759190	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73963094	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7568338	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7579392	1.00[CEU][hapmap]
rs7585876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7592963	1.00[CEU][hapmap]
rs7592987	1.00[CEU][hapmap]
rs7606229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817518	chr2:141714174-142287302	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv583203	chr2:142055133-142378975	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv875240	chr2:142199421-142347455	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
4	nsv875243	chr2:142219033-142259592	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	nsv459607	chr2:142226768-142263400	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	nsv583207	chr2:142226768-142263400	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
7	nsv459618	chr2:142246988-142263746	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	nsv583209	chr2:142246988-142263746	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	nsv470491	chr2:142254119-142299923	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
10	nsv821740	chr2:142255019-142259467	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
11	nsv834393	chr2:142256714-142431564	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142247800-142266200	Weak transcription	Brain Anterior Caudate	brain
2	chr2:142256400-142263600	Weak transcription	Brain Hippocampus Middle	brain
3	chr2:142257800-142259200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:142257800-142265800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:142258000-142265800	Weak transcription	Brain Substantia Nigra	brain
6	chr2:142258800-142260200	Enhancers	Dnd41	blood

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