Variant report

Variant	rs397254
Chromosome Location	chr20:14840438-14840439
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:14838738..14840500-chr20:14846618..14848612,2	MCF-7	breast:
2	chr20:14835355..14837300-chr20:14840386..14842306,2	MCF-7	breast:
3	chr20:14837652..14840600-chr20:14844675..14847639,2	MCF-7	breast:

Extended variants
information (count: 283 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs17197687	0.96[CEU][hapmap]
rs204093	0.96[CEU][hapmap]
rs204102	0.96[EUR][1000 genomes]
rs204104	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs204106	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs204107	0.95[EUR][1000 genomes]
rs204115	0.96[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs2210049	0.92[CEU][hapmap]
rs2224275	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs374589	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs376711	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs381016	0.84[EUR][1000 genomes]
rs386257	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs388996	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs389171	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs389667	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs396868	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs407097	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs408182	0.81[EUR][1000 genomes]
rs412485	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs416027	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs416233	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs426045	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs429156	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs432501	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs438632	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs439451	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs442467	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs443038	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs443597	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs444827	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs447564	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs448177	0.84[EUR][1000 genomes]
rs6042917	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6042962	0.92[CEU][hapmap];0.82[TSI][hapmap]
rs6110427	0.96[EUR][1000 genomes]
rs6110431	1.00[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs6135249	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs7352992	0.89[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap]
rs984968	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:243 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055499	chr20:14224873-14848061	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1059579	chr20:14518849-14941319	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1065590	chr20:14549721-14848061	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3512353	chr20:14560028-15087709	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3512354	chr20:14560087-15087661	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv585452	chr20:14569942-14986602	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv912695	chr20:14579703-14992542	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv585453	chr20:14609957-14936935	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv585454	chr20:14609957-14967506	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1066070	chr20:14627662-15180181	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1056497	chr20:14628216-14910061	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1060876	chr20:14629122-14875771	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv544189	chr20:14629122-14875771	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv868932	chr20:14629123-14928627	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv1062048	chr20:14633652-14887370	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	esv2751906	chr20:14658364-15026100	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
17	nsv949548	chr20:14667415-15125972	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
18	nsv948395	chr20:14667415-15161670	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
19	nsv585456	chr20:14668243-14954943	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv912698	chr20:14672177-14890211	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv912699	chr20:14672177-14901776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv1059534	chr20:14677058-14848061	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv544190	chr20:14677058-14848061	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv1058831	chr20:14677058-14941319	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
25	nsv544191	chr20:14677058-14941319	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
26	nsv458878	chr20:14681863-14890211	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
27	nsv585458	chr20:14681863-14890211	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
28	nsv912701	chr20:14682334-14848659	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
29	nsv912702	chr20:14686297-14853050	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
30	nsv1064226	chr20:14687769-14897602	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
31	esv1830386	chr20:14690185-14983868	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
32	nsv912706	chr20:14697386-14853050	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
33	nsv1062251	chr20:14698284-14859819	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
34	esv2422304	chr20:14699810-14926297	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
35	nsv1067404	chr20:14699839-14964658	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
36	nsv544192	chr20:14699839-14964658	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
37	nsv1057007	chr20:14700039-14964519	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
38	nsv544193	chr20:14700039-14964519	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
39	nsv916020	chr20:14700045-15134231	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
40	nsv1066982	chr20:14702890-14850905	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
41	nsv432103	chr20:14702900-14869900	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
42	esv2756830	chr20:14705888-14844049	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
43	esv2758784	chr20:14705888-14855457	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
44	nsv585462	chr20:14705888-14858910	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
45	nsv517845	chr20:14705888-14866618	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
46	nsv585463	chr20:14705888-14890211	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
47	nsv585464	chr20:14705888-15082546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
48	nsv585466	chr20:14706616-14862972	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
49	nsv1066377	chr20:14707770-15102827	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
50	nsv1059014	chr20:14707770-15103304	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:14825800-14845600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:14839000-14841000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr20:14839600-14842600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr20:14840000-14842400	Enhancers	GM12878-XiMat	blood
5	chr20:14840400-14840600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
6	chr20:14840400-14840800	Weak transcription	Brain Germinal Matrix	brain
7	chr20:14840400-14841000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr20:14840400-14841200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr20:14840400-14841800	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr20:14840400-14842200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
11	chr20:14840400-14842400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr20:14840400-14842400	Enhancers	HUES64 Cell Line	embryonic stem cell

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