Variant report

Variant	rs28540249
Chromosome Location	chr15:57942223-57942224
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57941609..57943527-chr15:57997998..57999551,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255529	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1290244	1.00[EUR][1000 genomes]
rs1540397	1.00[EUR][1000 genomes]
rs16953334	1.00[EUR][1000 genomes]
rs16977546	1.00[EUR][1000 genomes]
rs16977553	1.00[EUR][1000 genomes]
rs16977555	1.00[EUR][1000 genomes]
rs16977563	1.00[EUR][1000 genomes]
rs16977581	1.00[EUR][1000 genomes]
rs16977583	1.00[EUR][1000 genomes]
rs16977584	1.00[EUR][1000 genomes]
rs16977600	1.00[EUR][1000 genomes]
rs16977673	1.00[EUR][1000 genomes]
rs1834487	1.00[EUR][1000 genomes]
rs1946357	1.00[EUR][1000 genomes]
rs2098891	1.00[EUR][1000 genomes]
rs2554031	1.00[EUR][1000 genomes]
rs2733610	1.00[EUR][1000 genomes]
rs2733611	1.00[EUR][1000 genomes]
rs2733612	1.00[EUR][1000 genomes]
rs28547400	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28630067	1.00[EUR][1000 genomes]
rs28707698	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55769610	1.00[EUR][1000 genomes]
rs55782827	1.00[EUR][1000 genomes]
rs56091272	1.00[EUR][1000 genomes]
rs56810932	1.00[EUR][1000 genomes]
rs59333719	1.00[EUR][1000 genomes]
rs60234362	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60767381	1.00[EUR][1000 genomes]
rs60973024	1.00[EUR][1000 genomes]
rs6493944	1.00[EUR][1000 genomes]
rs6493948	1.00[EUR][1000 genomes]
rs7167118	1.00[EUR][1000 genomes]
rs7174233	1.00[EUR][1000 genomes]
rs7174359	1.00[EUR][1000 genomes]
rs7181645	1.00[EUR][1000 genomes]
rs73421901	1.00[EUR][1000 genomes]
rs73423507	1.00[EUR][1000 genomes]
rs73423512	1.00[EUR][1000 genomes]
rs73423518	1.00[EUR][1000 genomes]
rs73423522	1.00[EUR][1000 genomes]
rs73423541	1.00[EUR][1000 genomes]
rs73423555	1.00[EUR][1000 genomes]
rs73423558	1.00[EUR][1000 genomes]
rs73423560	1.00[EUR][1000 genomes]
rs73423562	1.00[EUR][1000 genomes]
rs73423566	1.00[EUR][1000 genomes]
rs73423591	1.00[EUR][1000 genomes]
rs74016229	1.00[EUR][1000 genomes]
rs74016236	1.00[EUR][1000 genomes]
rs74017953	1.00[EUR][1000 genomes]
rs74018224	1.00[EUR][1000 genomes]
rs8028953	1.00[EUR][1000 genomes]
rs933839	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv530682	chr15:57912502-58108285	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers 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	8 gene(s)	inside rSNPs	diseases
4	nsv1038667	chr15:57933076-58481870	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats 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	nsv542400	chr15:57933076-58481870	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 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	chr15:57919400-57946800	Weak transcription	Fetal Lung	lung
2	chr15:57919400-57959400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr15:57932200-57967400	Weak transcription	Aorta	Aorta
4	chr15:57933400-57982600	Weak transcription	Esophagus	oesophagus
5	chr15:57936600-57954000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr15:57937000-57944200	Weak transcription	Fetal Stomach	stomach
7	chr15:57937000-57946800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr15:57937200-57946600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:57938600-57944000	Genic enhancers	Fetal Heart	heart
10	chr15:57940000-57943800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr15:57940200-57942800	Weak transcription	Right Atrium	heart
12	chr15:57940200-57943200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr15:57940200-57943600	Weak transcription	Fetal Muscle Leg	muscle
14	chr15:57940200-57943600	Weak transcription	Lung	lung
15	chr15:57940200-57944600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:57940200-57945800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:57940200-57946800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr15:57940200-57955000	Weak transcription	Gastric	stomach
19	chr15:57940400-57946600	Weak transcription	Stomach Mucosa	stomach
20	chr15:57940800-57942400	Weak transcription	Left Ventricle	heart
21	chr15:57940800-57944600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr15:57940800-57946200	Weak transcription	Fetal Intestine Small	intestine
23	chr15:57940800-57955000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr15:57941200-57943400	Weak transcription	Right Ventricle	heart
25	chr15:57941600-57944600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:57941600-57946400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr15:57941600-57946400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr15:57941600-57954600	Weak transcription	Pancreas	Pancrea
29	chr15:57941600-57955000	Weak transcription	Psoas Muscle	Psoas
30	chr15:57942000-57943000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:57942000-57943600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:57942000-57943800	Strong transcription	Fetal Intestine Large	intestine
33	chr15:57942200-57942800	Genic enhancers	Adipose Nuclei	Adipose

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