Variant report

Variant	rs2574754
Chromosome Location	chr15:51124439-51124440
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	chr15:51123963..51125552-chr15:51144556..51147356,2	MCF-7	breast:

Extended variants
information (count: 119 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs11070812	0.81[ASN][1000 genomes]
rs11070822	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1135397	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1147132	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1147134	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1147138	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1147140	0.86[ASN][1000 genomes]
rs11636886	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12050528	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12148865	0.83[ASN][1000 genomes]
rs12440081	0.81[ASN][1000 genomes]
rs12440167	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12440387	0.95[AFR][1000 genomes]
rs12440570	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs12440745	0.90[AFR][1000 genomes]
rs12440864	0.94[JPT][hapmap]
rs12442145	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs12591438	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12592178	0.91[ASN][1000 genomes]
rs12592778	0.82[CHB][hapmap]
rs12593342	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12593765	0.95[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12593778	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap]
rs12595051	0.90[ASN][1000 genomes]
rs12595200	0.84[ASN][1000 genomes]
rs12595526	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap]
rs1276855	0.81[ASN][1000 genomes]
rs1276856	0.83[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs12899428	0.87[ASN][1000 genomes]
rs1290084	0.86[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs12902649	0.90[AFR][1000 genomes]
rs12904435	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12909760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12909839	0.95[AFR][1000 genomes]
rs12911207	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12916845	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17646025	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs17646461	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17646917	0.95[AFR][1000 genomes]
rs17702978	0.83[ASN][1000 genomes]
rs1871460	0.95[AFR][1000 genomes]
rs1876784	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs1903588	0.88[ASN][1000 genomes]
rs1903589	0.83[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs1904430	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes]
rs1955	0.95[AFR][1000 genomes]
rs2289304	0.95[CEU][hapmap]
rs2291107	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs2414057	0.83[ASN][1000 genomes]
rs2414063	0.85[CHB][hapmap]
rs2574756	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2614762	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2614765	0.83[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2614766	0.87[ASN][1000 genomes]
rs2614768	0.86[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2614774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2614788	1.00[AFR][1000 genomes]
rs2614793	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs2619689	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2619690	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2619695	0.89[ASN][1000 genomes]
rs2619696	0.97[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2663528	0.81[ASN][1000 genomes]
rs2663530	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2663531	1.00[AFR][1000 genomes]
rs2663532	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2663536	0.81[ASN][1000 genomes]
rs2663540	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2663542	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2663552	0.88[ASN][1000 genomes]
rs2663557	0.86[AFR][1000 genomes]
rs28565448	0.86[ASN][1000 genomes]
rs34991408	0.80[ASN][1000 genomes]
rs35088194	0.81[ASN][1000 genomes]
rs35473969	0.85[ASN][1000 genomes]
rs35573737	0.95[AFR][1000 genomes]
rs35862680	0.86[ASN][1000 genomes]
rs36004063	0.95[AFR][1000 genomes]
rs3784301	0.81[CHD][hapmap]
rs3784304	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs3825798	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs3848132	0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs4142324	0.82[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs56108218	0.82[ASN][1000 genomes]
rs57262951	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59486015	0.85[AFR][1000 genomes]
rs67889301	0.92[AFR][1000 genomes]
rs7179527	0.85[AFR][1000 genomes]
rs7181593	0.83[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs72742342	0.90[ASN][1000 genomes]
rs737031	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs8033807	0.82[ASN][1000 genomes]
rs8042982	0.81[ASN][1000 genomes]
rs8043017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8182062	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs936482	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:23 , 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	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	nsv516168	chr15:51114437-51217361	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2574754	TRPM7	cis	lymphoblastoid	seeQTL
rs2574754	SHF	cis	cerebellum	SCAN
rs2574754	SHC4	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51121400-51124800	Weak transcription	Fetal Kidney	kidney
2	chr15:51121600-51126800	Weak transcription	Stomach Mucosa	stomach
3	chr15:51121600-51132400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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