Variant report

Variant	rs56233400
Chromosome Location	chr15:55952452-55952453
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:55951550..55954249-chr15:56034622..56036474,2	MCF-7	breast:
2	chr15:55948243..55950096-chr15:55952230..55953920,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166450	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11853232	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1438914	0.82[EUR][1000 genomes]
rs16976434	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16976479	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2053335	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2414428	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs36016255	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4337238	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56190205	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56220110	0.84[AMR][1000 genomes]
rs720508	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73408312	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73408332	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73423329	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73423335	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs999303	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1049774	chr15:55759573-56044600	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv457158	chr15:55930542-55982257	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv569541	chr15:55930542-55982257	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55911800-55977000	Weak transcription	Fetal Intestine Small	intestine
2	chr15:55920600-55953400	Weak transcription	HUVEC	blood vessel
3	chr15:55920800-55987600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:55932600-55987000	Weak transcription	Ovary	ovary
5	chr15:55932800-55973400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:55933400-55953200	Weak transcription	HepG2	liver
7	chr15:55933400-55953400	Weak transcription	Fetal Intestine Large	intestine
8	chr15:55939200-55953400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:55942800-55974400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:55945000-55953200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr15:55946000-55953400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:55947400-55960200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:55948200-55953600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:55951200-55952800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:55951200-55953400	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr15:55951200-55953400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr15:55951200-55953400	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr15:55951200-55955400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr15:55951200-55956000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr15:55951400-55955600	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr15:55952000-55953200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr15:55952000-55953400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:55952000-55955200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:55952200-55960000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:55952400-55952800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:55952400-55953000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr15:55952400-55953600	Enhancers	Fetal Kidney	kidney
28	chr15:55952400-55954400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:55952400-55954600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr15:55952400-55955800	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr15:55952400-55957000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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