Variant report

Variant	rs17041561
Chromosome Location	chr2:111583762-111583763
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	chr2:111581367..111584584-chr2:111877642..111880944,3	MCF-7	breast:
2	chr2:111582825..111585419-chr2:111784404..111786190,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153094	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10203271	1.00[TSI][hapmap]
rs11900983	1.00[TSI][hapmap]
rs11903773	1.00[TSI][hapmap]
rs12474907	1.00[CEU][hapmap]
rs13386878	1.00[TSI][hapmap]
rs13388313	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs13398617	1.00[TSI][hapmap]
rs13410685	1.00[TSI][hapmap]
rs17041539	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17041553	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17041554	1.00[CEU][hapmap];0.89[GIH][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17041555	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28452164	0.82[EUR][1000 genomes]
rs34026418	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3817265	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4255970	0.82[EUR][1000 genomes]
rs55682108	0.82[EUR][1000 genomes]
rs55780486	1.00[EUR][1000 genomes]
rs55849112	0.82[EUR][1000 genomes]
rs55857945	0.82[EUR][1000 genomes]
rs55875504	0.82[EUR][1000 genomes]
rs55875530	0.82[EUR][1000 genomes]
rs55927063	0.82[EUR][1000 genomes]
rs56010803	1.00[EUR][1000 genomes]
rs56031628	0.82[EUR][1000 genomes]
rs56062220	0.82[EUR][1000 genomes]
rs56110941	0.82[EUR][1000 genomes]
rs56146538	0.82[EUR][1000 genomes]
rs56165253	0.82[EUR][1000 genomes]
rs56169320	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56177778	0.82[EUR][1000 genomes]
rs56181028	0.82[EUR][1000 genomes]
rs56238325	0.82[EUR][1000 genomes]
rs56260092	0.82[EUR][1000 genomes]
rs56272335	0.82[EUR][1000 genomes]
rs56281800	1.00[EUR][1000 genomes]
rs56289191	0.82[EUR][1000 genomes]
rs56320021	0.82[EUR][1000 genomes]
rs57101781	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57318054	0.82[EUR][1000 genomes]
rs57847126	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57862073	0.82[EUR][1000 genomes]
rs58054304	0.82[EUR][1000 genomes]
rs58569659	0.82[EUR][1000 genomes]
rs58588523	0.82[EUR][1000 genomes]
rs58719148	0.82[AFR][1000 genomes]
rs59258102	0.82[EUR][1000 genomes]
rs59413237	0.82[EUR][1000 genomes]
rs60185821	1.00[EUR][1000 genomes]
rs60357733	0.82[EUR][1000 genomes]
rs61124407	0.82[EUR][1000 genomes]
rs61376946	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66616139	0.82[EUR][1000 genomes]
rs72828843	0.82[EUR][1000 genomes]
rs72828844	0.82[EUR][1000 genomes]
rs72828845	0.82[EUR][1000 genomes]
rs72828846	0.82[EUR][1000 genomes]
rs72828849	0.82[EUR][1000 genomes]
rs72828851	0.82[EUR][1000 genomes]
rs72828852	0.82[EUR][1000 genomes]
rs72828854	0.82[EUR][1000 genomes]
rs72828856	0.82[EUR][1000 genomes]
rs72828857	0.82[EUR][1000 genomes]
rs72828859	0.82[EUR][1000 genomes]
rs72828861	0.82[EUR][1000 genomes]
rs72830976	0.82[EUR][1000 genomes]
rs72830979	0.82[EUR][1000 genomes]
rs72830980	0.82[EUR][1000 genomes]
rs72830982	0.82[EUR][1000 genomes]
rs72830984	0.82[EUR][1000 genomes]
rs72830985	0.82[EUR][1000 genomes]
rs72830986	0.82[EUR][1000 genomes]
rs72830989	0.82[EUR][1000 genomes]
rs72830993	0.82[EUR][1000 genomes]
rs72830997	0.82[EUR][1000 genomes]
rs72831000	0.82[EUR][1000 genomes]
rs72832803	0.82[EUR][1000 genomes]
rs72832804	0.82[EUR][1000 genomes]
rs72832809	0.82[EUR][1000 genomes]
rs72832810	0.82[EUR][1000 genomes]
rs72832813	0.82[EUR][1000 genomes]
rs72832815	0.82[EUR][1000 genomes]
rs72832816	0.82[EUR][1000 genomes]
rs72832817	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs72832818	0.82[EUR][1000 genomes]
rs72832820	1.00[EUR][1000 genomes]
rs72832821	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72832822	1.00[EUR][1000 genomes]
rs72832824	1.00[EUR][1000 genomes]
rs72832826	1.00[EUR][1000 genomes]
rs72832828	1.00[EUR][1000 genomes]
rs72832837	1.00[EUR][1000 genomes]
rs72832838	1.00[EUR][1000 genomes]
rs72832839	1.00[EUR][1000 genomes]
rs72832841	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72832842	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72832843	1.00[EUR][1000 genomes]
rs72832846	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72832854	0.82[EUR][1000 genomes]
rs73956471	0.82[AFR][1000 genomes]
rs7581640	1.00[TSI][hapmap]
rs7592058	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs7609252	1.00[TSI][hapmap]
rs977406	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs981196	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874839	chr2:111400934-111868010	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1008758	chr2:111415136-111626467	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv535890	chr2:111415136-111626467	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv997829	chr2:111486961-111780537	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111562800-111604000	Weak transcription	Lung	lung
2	chr2:111569400-111585000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:111569800-111590600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr2:111579000-111584400	Weak transcription	Fetal Thymus	thymus
5	chr2:111579200-111590600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:111581200-111584000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:111582000-111587000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:111582000-111591000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:111582200-111590800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:111582800-111590600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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