Variant report

Variant	rs28631249
Chromosome Location	chr15:52454887-52454888
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52453475..52455065-chr15:52470814..52473297,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069966	Chromatin interaction
ENSG00000259577	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10162634	0.93[ASN][1000 genomes]
rs10162876	0.93[ASN][1000 genomes]
rs10220890	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2414135	0.80[ASN][1000 genomes]
rs28380149	0.82[EUR][1000 genomes]
rs28409853	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28437132	0.88[AFR][1000 genomes]
rs28492876	0.91[ASN][1000 genomes]
rs28678248	0.80[ASN][1000 genomes]
rs28691169	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28703712	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28716893	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28765241	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28835411	0.94[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3829469	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4238386	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59851373	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61195644	0.94[ASN][1000 genomes]
rs73402875	0.92[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	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1047647	chr15:52425879-52469181	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52422600-52457600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:52423000-52458200	Weak transcription	Dnd41	blood
3	chr15:52429800-52470200	Weak transcription	Fetal Brain Male	brain
4	chr15:52430200-52457800	Weak transcription	Fetal Intestine Large	intestine
5	chr15:52432200-52455200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:52432200-52455200	Weak transcription	Colonic Mucosa	Colon
7	chr15:52436800-52457200	Weak transcription	GM12878-XiMat	blood
8	chr15:52437200-52456800	Weak transcription	HSMM	muscle
9	chr15:52437800-52463600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr15:52438000-52455000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:52439200-52463600	Weak transcription	NHEK	skin
12	chr15:52441000-52457400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr15:52442000-52455200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:52442000-52463600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:52442000-52463600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr15:52442200-52455800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:52442200-52470400	Weak transcription	Colon Smooth Muscle	Colon
18	chr15:52442200-52471000	Weak transcription	Brain Substantia Nigra	brain
19	chr15:52442200-52471000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:52442400-52457200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr15:52442400-52457200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr15:52442400-52457800	Weak transcription	Adipose Nuclei	Adipose
23	chr15:52442600-52470000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr15:52442600-52470400	Weak transcription	HMEC	breast
25	chr15:52443000-52470800	Weak transcription	Brain Hippocampus Middle	brain
26	chr15:52443400-52455400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:52443800-52455200	Weak transcription	Right Ventricle	heart
28	chr15:52443800-52455400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr15:52443800-52456000	Weak transcription	Fetal Lung	lung
30	chr15:52443800-52457000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:52443800-52463600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:52444000-52455200	Weak transcription	Brain Anterior Caudate	brain
33	chr15:52444000-52455800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:52444000-52457200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr15:52444000-52457400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:52444000-52457800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr15:52444000-52458000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr15:52444200-52455200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:52445600-52455200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr15:52445600-52455600	Weak transcription	Lung	lung
41	chr15:52445600-52463400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr15:52445600-52463600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:52445600-52471000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr15:52446000-52455400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr15:52447400-52460200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr15:52447400-52471000	Weak transcription	Right Atrium	heart
47	chr15:52447600-52463000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr15:52448000-52459800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr15:52448200-52457600	Weak transcription	Fetal Muscle Leg	muscle
50	chr15:52448800-52465200	Weak transcription	Liver	Liver

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