Variant report

Variant	rs9428515
Chromosome Location	chr1:241938718-241938719
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:241938342..241941213-chr1:241948458..241951421,2	MCF-7	breast:
2	chr1:241931182..241934991-chr1:241935809..241940192,4	K562	blood:
3	chr1:241801132..241803391-chr1:241936731..241938853,2	K562	blood:
4	chr1:241938483..241941296-chr1:241943224..241944927,2	K562	blood:

Variant related genes	Relation type
ENSG00000162843	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1017018	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10737867	0.81[ASN][1000 genomes]
rs10737868	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10737869	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10802990	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10926564	0.88[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10926569	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs11809239	0.88[ASN][1000 genomes]
rs12022825	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12038477	0.95[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs12042255	0.80[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs1418764	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1891566	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4129118	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4428871	0.96[ASN][1000 genomes]
rs4658661	0.83[JPT][hapmap]
rs55865277	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56396922	0.88[ASN][1000 genomes]
rs59836392	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6413961	0.91[JPT][hapmap]
rs6429300	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6429301	0.87[JPT][hapmap]
rs6429304	0.81[ASN][1000 genomes]
rs6429305	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6429312	0.94[ASN][1000 genomes]
rs6429313	0.96[ASN][1000 genomes]
rs6429314	0.95[ASN][1000 genomes]
rs6660811	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6666953	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6669036	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6669629	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6680142	0.86[JPT][hapmap]
rs6695661	0.86[JPT][hapmap]
rs6696527	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72755248	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72755251	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7418198	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7418599	0.86[JPT][hapmap]
rs7418764	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7526583	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7526586	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7530794	0.81[ASN][1000 genomes]
rs7530797	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7533622	0.95[ASN][1000 genomes]
rs7551270	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9428516	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9428520	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9428521	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9428524	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9428525	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9428527	0.95[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9428529	0.82[EUR][1000 genomes]
rs9428891	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9428892	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9428893	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9428894	0.85[CEU][hapmap]
rs9428898	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9428900	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs9428901	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9428902	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs952084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv948409	chr1:241830086-242489705	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv528015	chr1:241865219-242070731	Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1008300	chr1:241886514-242171611	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	esv2762521	chr1:241891040-242074222	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241937600-241940600	Weak transcription	Placenta	Placenta
2	chr1:241938000-241938800	Enhancers	K562	blood
3	chr1:241938600-241939200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr1:241938600-241940200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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