Variant report

Variant	rs72828859
Chromosome Location	chr2:111497543-111497544
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:111471612..111473359-chr2:111497038..111499262,2	MCF-7	breast:

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs13421709	0.90[ASN][1000 genomes]
rs17041539	0.82[EUR][1000 genomes]
rs17041553	0.82[EUR][1000 genomes]
rs17041554	0.82[EUR][1000 genomes]
rs17041555	0.82[EUR][1000 genomes]
rs17041561	0.82[EUR][1000 genomes]
rs28452164	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34026418	0.82[EUR][1000 genomes]
rs3817265	0.82[EUR][1000 genomes]
rs4255970	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55682108	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55780486	0.82[EUR][1000 genomes]
rs55849112	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55857945	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55875504	1.00[EUR][1000 genomes]
rs55875530	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55927063	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56010803	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56031628	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56062220	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56110941	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56146538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56165253	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56169320	0.82[EUR][1000 genomes]
rs56177778	1.00[EUR][1000 genomes]
rs56181028	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56202720	0.90[ASN][1000 genomes]
rs56238325	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56260092	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56272335	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56281800	0.82[EUR][1000 genomes]
rs56289191	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56320021	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57101781	0.82[EUR][1000 genomes]
rs57318054	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57847126	0.82[EUR][1000 genomes]
rs57862073	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58054304	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58569659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58588523	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59258102	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59413237	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60185821	0.82[EUR][1000 genomes]
rs60357733	1.00[EUR][1000 genomes]
rs61124407	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61376946	0.82[EUR][1000 genomes]
rs61637608	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66616139	1.00[EUR][1000 genomes]
rs72828836	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72828838	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72828843	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72828844	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72828845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72828846	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72828847	0.80[ASN][1000 genomes]
rs72828848	0.82[ASN][1000 genomes]
rs72828849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72828850	0.97[ASN][1000 genomes]
rs72828851	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72828852	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72828854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72828856	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72828857	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72828861	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72830976	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72830979	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72830980	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72830982	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72830984	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72830985	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72830986	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72830989	1.00[EUR][1000 genomes]
rs72830990	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72830993	1.00[EUR][1000 genomes]
rs72830995	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72830996	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72830997	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72831000	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72832803	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72832804	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72832809	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72832810	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72832813	1.00[EUR][1000 genomes]
rs72832815	1.00[EUR][1000 genomes]
rs72832816	1.00[EUR][1000 genomes]
rs72832817	1.00[EUR][1000 genomes]
rs72832818	1.00[EUR][1000 genomes]
rs72832820	0.82[EUR][1000 genomes]
rs72832821	0.82[EUR][1000 genomes]
rs72832822	0.82[EUR][1000 genomes]
rs72832824	0.82[EUR][1000 genomes]
rs72832826	0.82[EUR][1000 genomes]
rs72832828	0.82[EUR][1000 genomes]
rs72832837	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72832838	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72832839	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72832841	0.82[EUR][1000 genomes]
rs72832842	0.82[EUR][1000 genomes]
rs72832843	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72832846	0.82[EUR][1000 genomes]
rs977406	0.82[EUR][1000 genomes]
rs981196	0.82[EUR][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:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111493000-111498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:111493400-111498000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:111493400-111498400	Weak transcription	HMEC	breast
4	chr2:111493400-111498600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:111494600-111498000	Weak transcription	Placenta	Placenta
6	chr2:111495600-111498600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:111495800-111498200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:111495800-111498400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:111495800-111498400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:111496000-111498200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:111496000-111498400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:111496000-111498800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:111496400-111497800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:111496400-111498400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:111497000-111497800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:111497000-111499800	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr2:111497200-111499800	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr2:111497400-111499600	Weak transcription	Lung	lung

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