Variant report

Variant	rs1543398
Chromosome Location	chr20:15316664-15316665
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:14335576..14337791-chr20:15315333..15317078,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1014682	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1543399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2021764	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap]
rs2023504	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2023506	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2058828	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2245014	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2255548	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2423920	0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs2423921	0.83[ASN][1000 genomes]
rs2423922	0.92[YRI][hapmap]
rs2423923	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2423925	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2423928	0.86[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2423929	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2423935	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2423937	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2423942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2423943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2423944	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs2423945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2423946	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2423948	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2423949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2423950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2423951	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4814359	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4814360	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6034162	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6043218	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs764119	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs986421	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062252	chr20:14964258-15547739	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv544206	chr20:14964258-15547739	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv524481	chr20:15007730-15382919	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv916795	chr20:15041479-15345528	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1060275	chr20:15084485-15327541	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1058890	chr20:15234769-15388360	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv2755557	chr20:15250014-15323282	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv912788	chr20:15275538-15332749	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv912789	chr20:15275538-15352001	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv2757712	chr20:15282448-15331007	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv2758786	chr20:15282448-15331007	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1057619	chr20:15301890-15317978	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv3302	chr20:15302167-15324114	Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv1055943	chr20:15305258-15317978	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	esv2760674	chr20:15307955-15322241	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv817885	chr20:15308563-15317978	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	esv2577005	chr20:15310433-15321350	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv2599745	chr20:15310756-15321076	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
19	esv2388810	chr20:15310762-15320773	Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
20	esv3454538	chr20:15310806-15320773	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	esv3454536	chr20:15310857-15320745	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
22	esv3454539	chr20:15310857-15320745	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
23	esv3454537	chr20:15310867-15320690	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
24	esv15259	chr20:15310943-15320723	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
25	nsv1059700	chr20:15311358-15323282	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
26	nsv1058742	chr20:15311358-15323949	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
27	nsv442778	chr20:15311370-15317974	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
28	esv2421979	chr20:15311370-15318767	Active TSS Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
29	nsv514934	chr20:15311389-15317704	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
30	esv34824	chr20:15311400-15317218	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
31	nsv517450	chr20:15311431-15317978	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
32	nsv585629	chr20:15311431-15317978	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
33	nsv817886	chr20:15311431-15317978	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
34	esv3693286	chr20:15311431-15318767	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
35	nsv433174	chr20:15312796-15318767	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:15315800-15317800	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr20:15316000-15316800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr20:15316200-15317200	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr20:15316400-15316800	Enhancers	H9 Cell Line	embryonic stem cell
5	chr20:15316400-15316800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr20:15316400-15317400	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr20:15316400-15317600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr20:15316400-15317600	Enhancers	Placenta Amnion	Placenta Amnion
9	chr20:15316400-15317800	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr20:15316600-15316800	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr20:15316600-15317600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr20:15316600-15317600	Enhancers	HUES6 Cell Line	embryonic stem cell

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