Variant report

Variant	rs2997624
Chromosome Location	chr13:50581301-50581302
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50569577..50572074-chr13:50579319..50584996,5	MCF-7	breast:
2	chr13:50572788..50574418-chr13:50579406..50581918,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264864	Chromatin interaction
ENSG00000204977	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1326120	0.82[AMR][1000 genomes]
rs2066549	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2066557	0.84[ASN][1000 genomes]
rs2066558	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2066572	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2066575	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2066585	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2066587	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2066594	0.85[AMR][1000 genomes]
rs2242482	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2687951	0.85[AMR][1000 genomes]
rs2740508	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2740524	0.85[ASN][1000 genomes]
rs2740544	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2740545	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2760914	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2803839	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2812216	0.83[AMR][1000 genomes]
rs2812217	0.83[AMR][1000 genomes]
rs2812222	0.85[AMR][1000 genomes]
rs4548769	0.82[ASN][1000 genomes]
rs4942899	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4942901	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7336058	0.80[ASN][1000 genomes]
rs7338055	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9535407	0.82[ASN][1000 genomes]
rs9568354	0.81[ASN][1000 genomes]
rs9568363	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9568364	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9596215	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9596219	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9596220	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2997624	DLEU2	Cis_1M	lymphoblastoid	RTeQTL
rs2997624	DLEU2///DLEU2L	trans	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50571800-50585200	Weak transcription	Gastric	stomach
2	chr13:50572000-50585800	Weak transcription	Ovary	ovary
3	chr13:50572600-50589600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:50572800-50584400	Weak transcription	K562	blood
5	chr13:50573000-50594600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:50573800-50585000	Weak transcription	Left Ventricle	heart
7	chr13:50573800-50585800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr13:50573800-50588600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr13:50573800-50589400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr13:50573800-50590200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr13:50574000-50584800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr13:50574000-50585000	Weak transcription	Aorta	Aorta
13	chr13:50574000-50585600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr13:50574000-50586000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr13:50574000-50599600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr13:50574200-50589000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr13:50574200-50591000	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr13:50574600-50588800	Weak transcription	Stomach Mucosa	stomach
19	chr13:50574800-50584400	Weak transcription	Fetal Heart	heart
20	chr13:50574800-50584600	Weak transcription	Adipose Nuclei	Adipose
21	chr13:50574800-50584600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr13:50574800-50584600	Weak transcription	HMEC	breast
23	chr13:50574800-50585000	Weak transcription	NHEK	skin
24	chr13:50574800-50585800	Weak transcription	Fetal Kidney	kidney
25	chr13:50574800-50586200	Weak transcription	HepG2	liver
26	chr13:50574800-50588000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr13:50574800-50588600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr13:50575000-50586200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr13:50575200-50583400	Weak transcription	HUVEC	blood vessel
30	chr13:50575600-50588600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr13:50575800-50581400	Strong transcription	Fetal Muscle Trunk	muscle
32	chr13:50575800-50586400	Weak transcription	Hela-S3	cervix
33	chr13:50576200-50584600	Strong transcription	Fetal Intestine Small	intestine
34	chr13:50576400-50586400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr13:50576400-50589400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr13:50577200-50583400	Weak transcription	Lung	lung
37	chr13:50577200-50585000	Weak transcription	Right Ventricle	heart
38	chr13:50577200-50586200	Weak transcription	Psoas Muscle	Psoas
39	chr13:50577600-50585000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr13:50577600-50587600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr13:50577600-50594200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr13:50577600-50594400	Weak transcription	Fetal Brain Male	brain
43	chr13:50577800-50585800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr13:50578000-50581800	Weak transcription	Placenta	Placenta
45	chr13:50578000-50584400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr13:50578000-50596000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr13:50578200-50586200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr13:50578200-50590200	Strong transcription	Fetal Muscle Leg	muscle
49	chr13:50578400-50581800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr13:50578400-50584600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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