Variant report

Variant	rs2414058
Chromosome Location	chr15:51074199-51074200
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:51069319..51071729-chr15:51072874..51075260,2	MCF-7	breast:

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10744956	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11070809	0.86[JPT][hapmap]
rs11070824	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1147129	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1147131	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11635015	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11635102	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11855605	0.82[JPT][hapmap]
rs12438343	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12440387	0.81[CHB][hapmap]
rs12593469	0.82[JPT][hapmap]
rs12595754	0.99[ASN][1000 genomes]
rs1276854	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12900658	0.82[JPT][hapmap]
rs12903915	0.82[JPT][hapmap]
rs12909505	0.80[ASN][1000 genomes]
rs12915052	0.81[JPT][hapmap]
rs12915330	0.87[ASN][1000 genomes]
rs1472946	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1509423	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs17703090	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2127368	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2249535	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2306331	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2414081	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2614763	0.81[ASN][1000 genomes]
rs2614776	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2614779	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2614780	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2614781	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2614790	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2614791	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2614792	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2614794	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2619686	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2619691	0.86[CHB][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs2663533	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2663535	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2663538	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2663548	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2663550	0.83[ASN][1000 genomes]
rs2663551	0.81[ASN][1000 genomes]
rs2663553	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2663554	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2663556	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs28621809	0.82[ASN][1000 genomes]
rs3784301	0.91[JPT][hapmap]
rs3784302	0.90[JPT][hapmap]
rs3784303	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4775904	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4775910	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs5022760	0.82[JPT][hapmap]
rs60454952	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62018857	0.81[ASN][1000 genomes]
rs6493456	1.00[ASN][1000 genomes]
rs6493457	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6493469	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7162209	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7168385	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7168846	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7182865	0.81[JPT][hapmap]
rs7183434	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8024247	0.82[JPT][hapmap]
rs8027182	0.93[ASN][1000 genomes]
rs8029110	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8029155	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs8029369	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs8030214	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs8030680	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8031702	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs8033776	0.82[ASN][1000 genomes]
rs8035358	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs8035452	0.82[JPT][hapmap]
rs8035635	0.82[JPT][hapmap]
rs9920753	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053966	chr15:50715572-51133186	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv542383	chr15:50715572-51133186	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1043805	chr15:50715572-51208891	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv542384	chr15:50715572-51208891	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
5	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv1051990	chr15:50745814-51133186	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv457134	chr15:50770868-51184583	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
8	nsv471242	chr15:50770868-51184583	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
9	nsv569396	chr15:50770868-51184583	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
10	nsv457135	chr15:50770868-51189707	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
11	nsv569397	chr15:50770868-51189707	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
12	nsv1048621	chr15:50775451-51115535	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv1047039	chr15:50782070-51187804	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
14	nsv542385	chr15:50782070-51187804	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
15	nsv457136	chr15:50789125-51294995	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
16	nsv569398	chr15:50789125-51294995	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
17	nsv1036081	chr15:50818569-51097229	Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
18	nsv1055112	chr15:50822035-51133186	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
19	nsv1042372	chr15:50846461-51208891	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
20	nsv542386	chr15:50846461-51208891	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
21	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
22	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
23	nsv904212	chr15:50979738-51132170	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
24	nsv904213	chr15:51011402-51119731	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
25	nsv457137	chr15:51019117-51117524	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
26	nsv569402	chr15:51019117-51117524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
27	nsv529339	chr15:51048579-51270372	Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
28	esv15453	chr15:51072875-51086217	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2414058	LYSMD2	cis	parietal	SCAN
rs2414058	SLC30A4	cis	parietal	SCAN
rs2414058	TNFAIP8L3	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51070600-51075000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:51073000-51075600	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr15:51073000-51076000	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr15:51073400-51076400	Enhancers	Fetal Heart	heart
5	chr15:51074000-51074200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
6	chr15:51074000-51074600	Enhancers	K562	blood

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