Variant report

Variant	rs12088920
Chromosome Location	chr1:241873139-241873140
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:241872290..241875094-chr1:241880689..241882589,2	K562	blood:
2	chr1:241872709..241875051-chr1:241876691..241878407,2	K562	blood:
3	chr1:241866993..241870450-chr1:241870800..241873707,3	K562	blood:
4	chr1:241872967..241875360-chr1:241876691..241879967,3	K562	blood:
5	chr1:241802159..241804895-chr1:241872554..241874822,2	MCF-7	breast:
6	chr1:241799109..241806555-chr1:241863719..241873987,19	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203668	Chromatin interaction
ENSG00000054277	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10926568	1.00[CHB][hapmap]
rs12074374	1.00[CHB][hapmap]
rs12091633	1.00[CHB][hapmap]
rs12092919	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs12095445	1.00[CHB][hapmap]
rs13375989	1.00[CHB][hapmap]
rs1342867	1.00[CHB][hapmap]
rs3007744	1.00[CHB][hapmap]
rs4658798	1.00[CHB][hapmap]
rs61825802	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61825804	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61825806	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61825846	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429299	1.00[CHB][hapmap]
rs6429302	1.00[CHB][hapmap]
rs6429311	1.00[CHB][hapmap]
rs6660576	1.00[CHB][hapmap]
rs6660686	1.00[CHB][hapmap]
rs6663895	1.00[CHB][hapmap]
rs6667772	1.00[CHB][hapmap]
rs6670605	1.00[CHB][hapmap]
rs6694094	1.00[CHB][hapmap]
rs6698158	1.00[CHB][hapmap]
rs6703922	1.00[CHB][hapmap]
rs72768081	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72768087	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7414353	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514880	1.00[CHB][hapmap]
rs7533124	1.00[CHB][hapmap]
rs7552731	1.00[CHB][hapmap]
rs7554579	1.00[CHB][hapmap]
rs851777	1.00[CHB][hapmap]
rs9428890	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	esv2829981	chr1:241869867-241887181	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241871800-241879200	Weak transcription	NHEK	skin
2	chr1:241871800-241880200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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