Variant report

Variant	rs1575387
Chromosome Location	chr13:50331835-50331836
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	chr13:50303610..50306425-chr13:50331002..50333456,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11148161	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11148164	0.91[ASN][1000 genomes]
rs11148167	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12428108	0.81[ASN][1000 genomes]
rs12430539	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12584401	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12584560	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12864534	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12866447	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12868235	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12869900	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12875005	0.81[EUR][1000 genomes]
rs12876223	0.94[EUR][1000 genomes]
rs12876889	0.81[EUR][1000 genomes]
rs12877931	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1535543	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1581744	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1923730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236354	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34423763	0.81[EUR][1000 genomes]
rs35331571	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35672544	0.85[AMR][1000 genomes]
rs3742095	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4603448	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4643206	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4941657	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4942864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942870	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4942879	0.81[AMR][1000 genomes]
rs71428292	0.81[EUR][1000 genomes]
rs73194404	0.91[ASN][1000 genomes]
rs7446	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7987502	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7997798	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9526592	0.86[EUR][1000 genomes]
rs9526595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526600	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535315	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9535326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535332	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535333	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535337	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9535339	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535344	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9535345	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9535347	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9535352	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9535356	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9646001	0.83[AMR][1000 genomes];0.91[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1575387	KPNA3	Cis_1M	lymphoblastoid	RTeQTL
rs1575387	EBPL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
2	chr13:50273200-50333800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr13:50290000-50334000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr13:50294400-50333000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr13:50296600-50338600	Weak transcription	Ovary	ovary
6	chr13:50300600-50345600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr13:50302800-50333800	Weak transcription	Thymus	Thymus
8	chr13:50303200-50334000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr13:50306000-50351600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr13:50306200-50334200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr13:50306200-50336200	Weak transcription	Adipose Nuclei	Adipose
12	chr13:50306800-50333800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr13:50308000-50356000	Weak transcription	Fetal Kidney	kidney
14	chr13:50315200-50336000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr13:50317600-50343600	Weak transcription	Primary T cells from cord blood	blood
16	chr13:50318800-50333800	Weak transcription	NH-A	brain
17	chr13:50319600-50333600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr13:50319600-50334800	Weak transcription	Fetal Lung	lung
19	chr13:50320000-50333600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr13:50320000-50333600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr13:50320000-50333600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr13:50320400-50336800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr13:50320600-50332200	Weak transcription	Fetal Muscle Leg	muscle
24	chr13:50320600-50332600	Weak transcription	Fetal Brain Female	brain
25	chr13:50320600-50333000	Weak transcription	Fetal Intestine Large	intestine
26	chr13:50320600-50333600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr13:50320600-50333600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr13:50320600-50333600	Weak transcription	Fetal Intestine Small	intestine
29	chr13:50320600-50333800	Weak transcription	Brain Hippocampus Middle	brain
30	chr13:50320600-50333800	Weak transcription	Fetal Stomach	stomach
31	chr13:50320600-50334800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr13:50320600-50334800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr13:50320600-50337400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr13:50320600-50337800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr13:50320800-50333400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr13:50320800-50333800	Weak transcription	Primary B cells from cord blood	blood
37	chr13:50320800-50333800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr13:50320800-50340400	Weak transcription	HUVEC	blood vessel
39	chr13:50321000-50333400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr13:50321000-50363800	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr13:50321200-50333400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr13:50321200-50333600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr13:50321200-50333800	Weak transcription	Fetal Thymus	thymus
44	chr13:50321200-50333800	Weak transcription	Dnd41	blood
45	chr13:50324400-50333400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr13:50324400-50340400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr13:50324600-50333400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr13:50324600-50334600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr13:50324600-50350800	Weak transcription	HSMM	muscle
50	chr13:50324600-50351000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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