Variant report

Variant	rs55952634
Chromosome Location	chr15:57843819-57843820
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57837700..57840998-chr15:57842272..57845131,4	MCF-7	breast:
2	chr15:57841937..57843856-chr15:57845649..57847200,2	K562	blood:
3	chr15:57842103..57844129-chr15:57847997..57849787,2	K562	blood:
4	chr15:57842103..57844046-chr15:57847997..57849926,2	K562	blood:
5	chr15:57836929..57839560-chr15:57843156..57845372,2	K562	blood:

Variant related genes	Relation type
ENSG00000240874	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11856	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11856674	0.92[ASN][1000 genomes]
rs12439291	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439292	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12439665	0.92[ASN][1000 genomes]
rs12439793	0.92[ASN][1000 genomes]
rs1626448	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1630903	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1666572	0.90[EUR][1000 genomes]
rs1666573	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1690316	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1690317	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1690318	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17820431	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17820437	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17820449	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17820461	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17820467	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1908191	0.92[EUR][1000 genomes]
rs1908192	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2131730	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2131731	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2131733	0.89[EUR][1000 genomes]
rs2270487	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2270488	0.91[ASN][1000 genomes]
rs2279606	0.92[ASN][1000 genomes]
rs2635389	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2922231	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2922232	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2932208	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2932209	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2934418	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742963	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742964	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774961	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4774962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55916627	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56362917	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59368768	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66802357	0.97[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67336499	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166305	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171354	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7171360	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72741522	0.96[ASN][1000 genomes]
rs72741528	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8025786	0.94[ASN][1000 genomes]
rs8038795	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs937248	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv904255	chr15:57790436-57907574	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57802600-57846600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr15:57830000-57846400	Weak transcription	Brain Substantia Nigra	brain
3	chr15:57837800-57853000	Weak transcription	Colon Smooth Muscle	Colon
4	chr15:57839800-57847800	Enhancers	Fetal Intestine Large	intestine
5	chr15:57840000-57846600	Weak transcription	Ovary	ovary
6	chr15:57840400-57844600	Enhancers	Stomach Mucosa	stomach
7	chr15:57840600-57847400	Enhancers	Placenta Amnion	Placenta Amnion
8	chr15:57840800-57848000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:57840800-57849400	Enhancers	Fetal Muscle Leg	muscle
10	chr15:57841000-57847800	Enhancers	Right Atrium	heart
11	chr15:57841000-57848000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr15:57841000-57848600	Enhancers	HSMMtube	muscle
13	chr15:57841200-57847600	Enhancers	Left Ventricle	heart
14	chr15:57841800-57847200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:57842000-57847800	Enhancers	Fetal Intestine Small	intestine
16	chr15:57842400-57844200	Enhancers	HUVEC	blood vessel
17	chr15:57842400-57846000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr15:57842600-57845200	Enhancers	Fetal Kidney	kidney
19	chr15:57842800-57844000	Enhancers	Right Ventricle	heart
20	chr15:57842800-57845200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:57842800-57845400	Enhancers	Adipose Nuclei	Adipose
22	chr15:57842800-57847600	Enhancers	HMEC	breast
23	chr15:57842800-57848600	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr15:57843000-57845200	Enhancers	NH-A	brain
25	chr15:57843000-57846800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:57843000-57847400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:57843000-57847600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:57843000-57847600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:57843000-57847600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr15:57843000-57847800	Enhancers	Gastric	stomach
31	chr15:57843000-57848400	Enhancers	Placenta	Placenta
32	chr15:57843000-57848600	Enhancers	Fetal Lung	lung
33	chr15:57843200-57844000	Enhancers	NHEK	skin
34	chr15:57843200-57844400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:57843200-57844400	Enhancers	Esophagus	oesophagus
36	chr15:57843200-57844600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:57843200-57844600	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr15:57843200-57844600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:57843200-57844800	Enhancers	Muscle Satellite Cultured Cells	--
40	chr15:57843200-57845200	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr15:57843200-57845200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr15:57843200-57845400	Enhancers	Fetal Muscle Trunk	muscle
43	chr15:57843200-57847600	Enhancers	Lung	lung
44	chr15:57843400-57844400	Strong transcription	Liver	Liver
45	chr15:57843400-57844600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr15:57843400-57844600	Enhancers	Spleen	Spleen
47	chr15:57843400-57844600	Enhancers	HepG2	liver
48	chr15:57843400-57844800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:57843400-57844800	Flanking Active TSS	A549	lung
50	chr15:57843400-57844800	Flanking Active TSS	Hela-S3	cervix

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