Variant report

Variant	rs1546394
Chromosome Location	chr3:161267774-161267775
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	chr3:161258952..161261503-chr3:161267723..161269425,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10936229	0.92[CEU][hapmap]
rs13433795	0.92[CEU][hapmap]
rs1450533	0.90[EUR][1000 genomes]
rs1506480	0.91[CEU][hapmap]
rs1506481	0.92[CEU][hapmap]
rs1546396	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546397	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1546398	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1905532	0.91[CEU][hapmap];0.92[CHB][hapmap]
rs1960516	0.90[EUR][1000 genomes]
rs41386047	0.91[CEU][hapmap]
rs4263306	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4856708	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56375427	0.90[EUR][1000 genomes]
rs62279585	1.00[EUR][1000 genomes]
rs62279587	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62281467	0.90[EUR][1000 genomes]
rs62281468	0.90[EUR][1000 genomes]
rs6441379	0.92[CEU][hapmap]
rs6441380	0.91[CEU][hapmap]
rs6441381	0.92[CEU][hapmap]
rs6762110	0.81[CEU][hapmap]
rs6773923	0.92[CEU][hapmap]
rs6803152	0.88[CEU][hapmap]
rs73166070	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73166073	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7621624	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621696	0.90[EUR][1000 genomes]
rs7624657	0.92[CEU][hapmap]
rs7624747	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs7632851	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7635683	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636548	0.92[CEU][hapmap]
rs7648970	0.91[CEU][hapmap]
rs869772	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs872677	0.91[CEU][hapmap]
rs937811	0.92[CEU][hapmap]
rs9811902	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9821882	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9831011	0.90[EUR][1000 genomes]
rs9847876	0.91[CEU][hapmap]
rs9848624	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9854509	0.90[CEU][hapmap];0.80[CHB][hapmap]
rs9859309	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867861	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9877005	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[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	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
2	nsv829773	chr3:161150422-161315189	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv829774	chr3:161229405-161386919	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2422309	chr3:161242389-161425932	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161266400-161274200	Weak transcription	Dnd41	blood
2	chr3:161266600-161270400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:161267000-161268800	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:161267200-161270200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:161267400-161267800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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