Variant report

Variant	rs28558576
Chromosome Location	chr15:55471377-55471378
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:55470856..55473009-chr15:55473749..55475937,3	K562	blood:
2	chr15:55469341..55471788-chr15:55488673..55490223,2	MCF-7	breast:
3	chr15:55468427..55470541-chr15:55470610..55476298,5	K562	blood:
4	chr15:55469036..55471417-chr15:55477962..55479850,2	K562	blood:
5	chr15:55468607..55473383-chr15:55473749..55481384,11	K562	blood:

Variant related genes	Relation type
ENSG00000137876	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10162819	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10162843	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1050931	0.80[ASN][1000 genomes]
rs10518804	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1061822	0.83[ASN][1000 genomes]
rs1061823	0.83[ASN][1000 genomes]
rs1061824	0.83[ASN][1000 genomes]
rs1061870	0.83[ASN][1000 genomes]
rs1061873	0.83[ASN][1000 genomes]
rs11852763	0.83[ASN][1000 genomes]
rs11855907	0.83[ASN][1000 genomes]
rs11855973	0.83[ASN][1000 genomes]
rs11855978	0.80[ASN][1000 genomes]
rs11857087	0.92[ASN][1000 genomes]
rs12385963	0.92[ASN][1000 genomes]
rs13380400	0.83[ASN][1000 genomes]
rs13733	0.89[ASN][1000 genomes]
rs16976036	0.89[ASN][1000 genomes]
rs16976039	0.89[ASN][1000 genomes]
rs16976065	0.96[ASN][1000 genomes]
rs16976083	0.93[ASN][1000 genomes]
rs16976094	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976116	0.90[ASN][1000 genomes]
rs16976149	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28433503	0.80[ASN][1000 genomes]
rs28449712	0.80[ASN][1000 genomes]
rs28489312	0.83[ASN][1000 genomes]
rs28508034	0.80[ASN][1000 genomes]
rs28526269	0.80[ASN][1000 genomes]
rs28530662	0.80[ASN][1000 genomes]
rs28535372	0.80[ASN][1000 genomes]
rs28541469	0.80[ASN][1000 genomes]
rs28562431	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28564077	0.82[ASN][1000 genomes]
rs28589384	0.83[ASN][1000 genomes]
rs28591259	0.80[ASN][1000 genomes]
rs28592928	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28600759	0.91[ASN][1000 genomes]
rs28630909	0.80[ASN][1000 genomes]
rs28636526	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28649719	0.80[ASN][1000 genomes]
rs28673043	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28699327	0.80[ASN][1000 genomes]
rs28704109	0.83[ASN][1000 genomes]
rs28706531	0.92[ASN][1000 genomes]
rs28708989	0.80[ASN][1000 genomes]
rs28710976	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28714578	0.83[ASN][1000 genomes]
rs2899580	0.83[ASN][1000 genomes]
rs2899581	0.83[ASN][1000 genomes]
rs2899582	0.83[ASN][1000 genomes]
rs3179664	0.83[ASN][1000 genomes]
rs3759861	0.93[ASN][1000 genomes]
rs3759862	0.92[ASN][1000 genomes]
rs3809539	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3809540	0.89[ASN][1000 genomes]
rs4238316	1.00[ASN][1000 genomes]
rs4503734	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4545742	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62020115	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6493768	0.92[ASN][1000 genomes]
rs7165491	0.80[ASN][1000 genomes]
rs7168472	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7168737	0.80[ASN][1000 genomes]
rs7172108	0.80[ASN][1000 genomes]
rs7172289	0.80[ASN][1000 genomes]
rs7179365	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7180594	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8027098	0.83[ASN][1000 genomes]
rs8030981	0.80[ASN][1000 genomes]
rs8031949	0.83[ASN][1000 genomes]
rs8033588	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8034063	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8034402	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8034853	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8034882	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8035625	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8043029	0.92[ASN][1000 genomes]
rs9300	0.89[ASN][1000 genomes]
rs9920165	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043176	chr15:55010228-55563000	Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1042741	chr15:55068022-55622497	Strong transcription Weak transcription Flanking Active TSS Enhancers 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	31 gene(s)	inside rSNPs	diseases
3	nsv1039471	chr15:55137606-55552555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv525768	chr15:55466155-55485494	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55455800-55487200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:55462600-55471600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr15:55462600-55488600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:55463200-55472400	Weak transcription	Ovary	ovary
5	chr15:55463200-55474600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:55463400-55472200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:55463800-55472600	Weak transcription	Fetal Kidney	kidney
8	chr15:55464600-55472400	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:55464800-55488200	Weak transcription	Lung	lung
10	chr15:55465400-55471400	Weak transcription	Brain Angular Gyrus	brain
11	chr15:55465400-55472600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr15:55465400-55476600	Weak transcription	Brain Anterior Caudate	brain
13	chr15:55465800-55471600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr15:55466600-55471400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr15:55466600-55472000	Weak transcription	Placenta	Placenta
16	chr15:55466800-55474000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr15:55466800-55474600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr15:55466800-55486800	Weak transcription	Psoas Muscle	Psoas
19	chr15:55467600-55472400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:55467800-55480600	Weak transcription	Fetal Stomach	stomach
21	chr15:55468000-55482000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:55468200-55481600	Weak transcription	Fetal Intestine Small	intestine
23	chr15:55468400-55471400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr15:55468400-55471600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr15:55468400-55472400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr15:55468600-55471600	Weak transcription	NHDF-Ad	bronchial
27	chr15:55468600-55471800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:55468600-55474600	Weak transcription	Brain Substantia Nigra	brain
29	chr15:55468800-55487000	Weak transcription	Gastric	stomach
30	chr15:55469000-55472000	Weak transcription	HSMMtube	muscle
31	chr15:55469000-55474400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr15:55469000-55477200	Strong transcription	Primary T cells from cord blood	blood
33	chr15:55469000-55481800	Weak transcription	Spleen	Spleen
34	chr15:55469200-55471600	Weak transcription	HMEC	breast
35	chr15:55469200-55472400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:55469200-55477200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr15:55469200-55484800	Strong transcription	Liver	Liver
38	chr15:55469200-55485000	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr15:55469400-55471600	Weak transcription	Fetal Muscle Leg	muscle
40	chr15:55469400-55471600	Weak transcription	Right Ventricle	heart
41	chr15:55469400-55472600	Weak transcription	NHLF	lung
42	chr15:55469400-55478000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:55469400-55485200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:55469600-55471400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr15:55469600-55473000	Strong transcription	Aorta	Aorta
46	chr15:55469600-55473200	Strong transcription	Thymus	Thymus
47	chr15:55469600-55474000	Weak transcription	Colonic Mucosa	Colon
48	chr15:55469600-55479600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr15:55469600-55485000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr15:55469600-55485200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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