Variant report

Variant	rs9526600
Chromosome Location	chr13:50350929-50350930
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	chr13:50349733..50352662-chr13:50364217..50367183,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102753	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11148160	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11148161	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11148163	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11148167	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12584560	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12866447	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12868235	0.85[ASN][1000 genomes]
rs12869900	0.89[EUR][1000 genomes]
rs12876223	0.86[EUR][1000 genomes]
rs1535543	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1575387	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1581744	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1923730	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2236354	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3742095	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4643206	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4941657	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4942864	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7987502	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526595	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535302	0.86[EUR][1000 genomes]
rs9535309	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9535326	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535332	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535333	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535337	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535339	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9646001	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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	nsv900072	chr13:50266109-50381016	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv900073	chr13:50286218-50381016	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv1818134	chr13:50306897-50374102	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv900074	chr13:50317104-50381016	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1038	chr13:50324773-50359990	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv900075	chr13:50331992-50376858	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9526600	KPNA3	Cis_1M	lymphoblastoid	RTeQTL
rs9526600	EBPL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50306000-50351600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr13:50308000-50356000	Weak transcription	Fetal Kidney	kidney
3	chr13:50321000-50363800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr13:50324600-50351000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr13:50334000-50352200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr13:50334200-50351200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr13:50334400-50351400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr13:50335000-50356400	Weak transcription	Primary B cells from cord blood	blood
9	chr13:50336200-50364800	Weak transcription	Fetal Intestine Small	intestine
10	chr13:50336400-50351600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr13:50336600-50352400	Weak transcription	Thymus	Thymus
12	chr13:50336600-50353800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr13:50336800-50364600	Weak transcription	NHLF	lung
14	chr13:50338000-50353800	Weak transcription	Dnd41	blood
15	chr13:50339200-50353800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr13:50339200-50355800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr13:50339200-50358800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr13:50339800-50358800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr13:50340600-50351200	Weak transcription	A549	lung
20	chr13:50341200-50359400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr13:50343400-50351800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr13:50344000-50355600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr13:50345400-50351200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr13:50345800-50351400	Weak transcription	GM12878-XiMat	blood
25	chr13:50346000-50351600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr13:50346200-50351600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr13:50347000-50351600	Weak transcription	Psoas Muscle	Psoas
28	chr13:50348600-50351600	Enhancers	Liver	Liver
29	chr13:50349200-50351600	Weak transcription	Pancreas	Pancrea
30	chr13:50349600-50352400	Weak transcription	Right Atrium	heart
31	chr13:50349600-50353600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr13:50349600-50357600	Weak transcription	Gastric	stomach
33	chr13:50349600-50357600	Weak transcription	Left Ventricle	heart
34	chr13:50349600-50365400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr13:50349600-50365400	Weak transcription	Lung	lung
36	chr13:50349800-50351000	Weak transcription	NHDF-Ad	bronchial
37	chr13:50349800-50351800	Weak transcription	HepG2	liver
38	chr13:50349800-50355200	Weak transcription	Fetal Heart	heart
39	chr13:50350000-50351000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr13:50350000-50353800	Weak transcription	Brain Substantia Nigra	brain
41	chr13:50350200-50351200	Weak transcription	Stomach Mucosa	stomach
42	chr13:50350200-50351800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr13:50350200-50352600	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr13:50350400-50356200	Weak transcription	Ovary	ovary
45	chr13:50350600-50351600	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr13:50350600-50351800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr13:50350600-50358600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr13:50350800-50351200	Enhancers	HSMM	muscle
49	chr13:50350800-50351600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr13:50350800-50351600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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