Variant report

Variant	rs28668028
Chromosome Location	chr15:31756657-31756658
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31747904..31750478-chr15:31754531..31757245,2	MCF-7	breast:

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1017720	0.83[EUR][1000 genomes]
rs1077169	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071075	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071076	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12148161	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12148181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439019	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12439195	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439214	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12439216	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12439310	0.82[EUR][1000 genomes]
rs12440316	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441399	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12441529	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441571	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12441588	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12441627	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12443255	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12592099	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12592342	0.94[ASN][1000 genomes]
rs12592371	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12595455	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1380235	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17228303	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17228317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17815977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008020	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2125617	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2125618	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2219508	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2338683	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28366602	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28367155	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28379435	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28392564	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28403178	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28421719	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28470561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28533482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28549906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28557161	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28579624	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28619436	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28623261	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28633343	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28633823	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28644187	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28655541	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28673491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28683761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28685794	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28687203	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28696791	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28703622	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716634	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28825540	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28896251	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35643888	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4238555	0.94[ASN][1000 genomes]
rs4401013	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4414458	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4451913	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4497646	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4611410	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4611411	0.82[ASN][1000 genomes]
rs4779528	0.94[ASN][1000 genomes]
rs4779529	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4779530	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4779531	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4779534	0.89[EUR][1000 genomes]
rs4779881	0.96[ASN][1000 genomes]
rs4779882	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55806858	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56008248	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56332002	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56349550	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62037907	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493688	0.83[EUR][1000 genomes]
rs6493689	0.82[EUR][1000 genomes]
rs7403275	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7403458	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs755809	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs755812	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8023660	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023664	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023790	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8035018	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038667	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8038953	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040186	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs971330	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs971331	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs971332	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv903840	chr15:31589970-31800149	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1051589	chr15:31728004-31972706	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv542320	chr15:31728004-31972706	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv469633	chr15:31731003-31904613	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv482330	chr15:31731003-31904613	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv903844	chr15:31736091-31781988	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1046271	chr15:31741255-31795961	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv903845	chr15:31751664-31939001	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv3420403	chr15:31754610-31756808	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31749200-31764000	Weak transcription	Right Atrium	heart
2	chr15:31751800-31756800	Weak transcription	NHEK	skin
3	chr15:31751800-31757800	Weak transcription	A549	lung
4	chr15:31752000-31756800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:31752000-31756800	Weak transcription	HMEC	breast
6	chr15:31752000-31763800	Weak transcription	Primary T cells from cord blood	blood
7	chr15:31753600-31757200	Weak transcription	Hela-S3	cervix
8	chr15:31754400-31757000	Weak transcription	Right Ventricle	heart
9	chr15:31754400-31761000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr15:31755200-31756800	Enhancers	Colonic Mucosa	Colon
11	chr15:31755800-31757000	Enhancers	Small Intestine	intestine
12	chr15:31755800-31757800	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr15:31755800-31758000	Enhancers	Stomach Mucosa	stomach
14	chr15:31755800-31758200	Enhancers	Esophagus	oesophagus
15	chr15:31756000-31756800	Enhancers	GM12878-XiMat	blood
16	chr15:31756200-31757000	Enhancers	Primary B cells from cord blood	blood
17	chr15:31756400-31757200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:31756400-31757600	Enhancers	Primary B cells from peripheral blood	blood
19	chr15:31756400-31757600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr15:31756600-31757000	Enhancers	Duodenum Mucosa	Duodenum
21	chr15:31756600-31757600	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr15:31756600-31757800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:31756600-31757800	Enhancers	Spleen	Spleen
24	chr15:31756600-31758400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:31756600-31758400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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