Variant report

Variant	rs16846484
Chromosome Location	chr2:142319677-142319678
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	chr2:142317711..142321512-chr2:142324977..142327310,3	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10928111	0.81[EUR][1000 genomes]
rs11681928	1.00[CHB][hapmap]
rs12467062	0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs12468830	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12469217	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12470072	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12470665	0.86[JPT][hapmap]
rs12476668	0.80[EUR][1000 genomes]
rs12476844	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12477753	0.85[JPT][hapmap]
rs12478973	0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs12612624	1.00[CHB][hapmap]
rs12615716	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12615851	0.91[CHB][hapmap]
rs12621499	0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13030335	0.96[JPT][hapmap]
rs13031144	1.00[JPT][hapmap]
rs1483141	0.83[JPT][hapmap]
rs16846467	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846506	0.83[CHB][hapmap]
rs16846521	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16846522	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16846530	0.95[CHB][hapmap]
rs2170668	1.00[CHB][hapmap]
rs2200192	0.87[JPT][hapmap]
rs2381190	1.00[CHB][hapmap]
rs2890615	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4384715	0.82[JPT][hapmap]
rs4544370	0.82[JPT][hapmap]
rs4574055	1.00[JPT][hapmap]
rs57933129	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6429908	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs72852491	0.80[EUR][1000 genomes]
rs72853570	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72855407	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72855428	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7562751	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7588818	0.87[JPT][hapmap]
rs7589997	0.81[EUR][1000 genomes]
rs7593962	0.86[JPT][hapmap]
rs7597633	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv459640	chr2:142291211-142345574	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
5	nsv583213	chr2:142291211-142345574	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
6	nsv583214	chr2:142299923-142458316	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
7	nsv1011019	chr2:142314999-142430460	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142315200-142322600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr2:142315200-142327800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:142315400-142320000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:142318200-142322200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:142318200-142322600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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