Variant report

Variant	rs28403229
Chromosome Location	chr15:50430325-50430326
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50428036..50430534-chr15:50437642..50439457,2	MCF-7	breast:
2	chr15:50420970..50423759-chr15:50428011..50430538,2	MCF-7	breast:
3	chr15:50425943..50428562-chr15:50428956..50430506,3	K562	blood:
4	chr15:50429608..50431277-chr15:50435108..50437577,2	K562	blood:
5	chr15:50168681..50169642-chr15:50430274..50431207,4	MCF-7	breast:
6	chr15:50330960..50333313-chr15:50430196..50432185,2	MCF-7	breast:
7	chr15:50168979..50170922-chr15:50428589..50430451,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104043	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10152738	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10519262	0.82[ASN][1000 genomes]
rs11070750	0.99[ASN][1000 genomes]
rs11070751	0.81[ASN][1000 genomes]
rs11070752	0.96[ASN][1000 genomes]
rs11631433	0.97[ASN][1000 genomes]
rs11632133	0.81[ASN][1000 genomes]
rs12439182	0.81[ASN][1000 genomes]
rs12442998	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12443171	0.81[ASN][1000 genomes]
rs12591791	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901981	0.83[ASN][1000 genomes]
rs12902997	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915230	0.81[ASN][1000 genomes]
rs12915287	0.99[ASN][1000 genomes]
rs2414025	0.80[ASN][1000 genomes]
rs28650901	0.96[ASN][1000 genomes]
rs4774556	0.99[ASN][1000 genomes]
rs5025069	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61214575	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7165446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7177316	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7178278	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8023371	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8036777	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8037555	0.99[ASN][1000 genomes]
rs933854	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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv569395	chr15:50345393-50437494	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv904208	chr15:50428495-50457858	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50425800-50430800	Enhancers	NHDF-Ad	bronchial
2	chr15:50426000-50430600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr15:50426000-50430800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr15:50426400-50430400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr15:50426400-50430400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr15:50426400-50430600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:50426400-50430600	Enhancers	NHLF	lung
8	chr15:50426400-50430800	Enhancers	Osteobl	bone
9	chr15:50427800-50436400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:50428400-50430400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:50428800-50430600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:50428800-50432400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:50429000-50430800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:50429000-50434200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr15:50429000-50437000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr15:50429000-50437600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr15:50429200-50430400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr15:50429200-50430400	Enhancers	K562	blood
19	chr15:50429200-50430600	Enhancers	NHEK	skin
20	chr15:50429200-50430800	Enhancers	HMEC	breast
21	chr15:50429400-50430400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:50429600-50430800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:50429600-50434600	Weak transcription	Colon Smooth Muscle	Colon
24	chr15:50429800-50430400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:50429800-50430400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:50429800-50430400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:50429800-50430400	Enhancers	HUVEC	blood vessel
28	chr15:50429800-50430400	Enhancers	NH-A	brain
29	chr15:50429800-50430600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:50429800-50431800	Weak transcription	Fetal Stomach	stomach
31	chr15:50430000-50432200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr15:50430200-50431200	Enhancers	A549	lung
33	chr15:50430200-50433600	Enhancers	Hela-S3	cervix

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