Variant report

Variant	rs12038477
Chromosome Location	chr1:241994183-241994184
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:241802310..241805173-chr1:241993132..241995327,2	K562	blood:

Variant related genes	Relation type
ENSG00000054277	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1017018	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10737868	0.90[CEU][hapmap];0.85[JPT][hapmap]
rs10926569	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs12022825	0.90[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12042255	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418764	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1891566	0.84[EUR][1000 genomes]
rs4129118	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs4658661	0.81[JPT][hapmap]
rs55865277	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59836392	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6413961	0.80[JPT][hapmap]
rs6666953	0.85[JPT][hapmap]
rs6669036	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs6669629	0.90[CEU][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs6696527	0.90[CEU][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap]
rs72755248	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72755251	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7418198	0.90[CEU][hapmap];0.85[JPT][hapmap]
rs7418764	0.90[CEU][hapmap];0.85[JPT][hapmap]
rs7530797	0.90[CEU][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap]
rs7551270	0.90[CEU][hapmap];0.85[JPT][hapmap]
rs9428515	0.95[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs9428516	0.84[EUR][1000 genomes]
rs9428520	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9428521	0.95[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9428524	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9428525	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9428527	0.90[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9428529	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9428891	0.83[EUR][1000 genomes]
rs9428892	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9428893	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9428894	0.81[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs9428898	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9428899	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9428900	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9428901	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9428902	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952084	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
10	nsv873373	chr1:241939069-242027500	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv873374	chr1:241975147-242097624	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv945406	chr1:241992115-241996420	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	3 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	chr1:241992400-242000800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:241992600-241995800	Weak transcription	A549	lung
3	chr1:241992800-241995400	Weak transcription	K562	blood
4	chr1:241994000-241994200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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