Variant report

Variant	rs12864534
Chromosome Location	chr13:50300130-50300131
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	chr13:50283454..50285237-chr13:50298897..50300982,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11148160	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11148167	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12430539	0.91[AFR][1000 genomes]
rs12584401	0.91[AFR][1000 genomes]
rs12866447	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12868235	0.91[AFR][1000 genomes]
rs12869900	0.83[EUR][1000 genomes]
rs12875005	0.91[EUR][1000 genomes]
rs12876223	0.81[EUR][1000 genomes]
rs12876889	0.92[EUR][1000 genomes]
rs12877931	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535543	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1575387	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1923730	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2025264	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2146143	0.91[ASN][1000 genomes]
rs2236354	0.91[AFR][1000 genomes]
rs34423763	0.92[EUR][1000 genomes]
rs35331571	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742095	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4603448	0.91[AFR][1000 genomes]
rs4643206	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4941657	0.91[AFR][1000 genomes]
rs4942864	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4942870	0.91[AFR][1000 genomes]
rs6561550	0.91[ASN][1000 genomes]
rs6561552	0.91[ASN][1000 genomes]
rs6561553	0.87[ASN][1000 genomes]
rs73192666	0.91[ASN][1000 genomes]
rs7446	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997798	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942032	0.91[ASN][1000 genomes]
rs9526592	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526595	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9535287	0.82[ASN][1000 genomes]
rs9535301	0.98[ASN][1000 genomes]
rs9535302	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535309	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535326	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9535333	0.86[EUR][1000 genomes]
rs9535339	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9535344	0.81[AFR][1000 genomes]
rs9535345	0.81[AFR][1000 genomes]
rs9535347	0.91[AFR][1000 genomes]
rs9535352	0.91[AFR][1000 genomes]
rs9535356	0.91[AFR][1000 genomes]
rs9568309	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12864534	KPNA3	Cis_1M	lymphoblastoid	RTeQTL
rs12864534	EBPL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266200-50307800	Weak transcription	Gastric	stomach
2	chr13:50266200-50316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
4	chr13:50273200-50326000	Weak transcription	Aorta	Aorta
5	chr13:50273200-50333800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr13:50276000-50307600	Weak transcription	Pancreas	Pancrea
7	chr13:50277000-50318400	Weak transcription	Hela-S3	cervix
8	chr13:50280000-50308000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr13:50290000-50304600	Strong transcription	Liver	Liver
10	chr13:50290000-50306200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr13:50290000-50306800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr13:50290000-50324000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr13:50290000-50334000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr13:50290200-50304600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr13:50290200-50316800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr13:50290400-50306800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr13:50290400-50307200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr13:50290600-50304400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr13:50290800-50301400	Strong transcription	Placenta	Placenta
20	chr13:50290800-50302600	Strong transcription	Adipose Nuclei	Adipose
21	chr13:50290800-50304200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr13:50291000-50301200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr13:50291000-50301200	Strong transcription	HSMM	muscle
24	chr13:50291000-50306800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr13:50291000-50306800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr13:50291200-50300600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr13:50291200-50301400	Strong transcription	Dnd41	blood
28	chr13:50292000-50300600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr13:50292600-50301800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr13:50293000-50304200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr13:50293200-50301000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr13:50293200-50326000	Weak transcription	Fetal Brain Male	brain
33	chr13:50294200-50305400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr13:50294200-50315000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr13:50294200-50324000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr13:50294400-50333000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr13:50294600-50301200	Strong transcription	Fetal Muscle Leg	muscle
38	chr13:50294800-50314200	Weak transcription	Stomach Mucosa	stomach
39	chr13:50295200-50301000	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr13:50296200-50307600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr13:50296200-50330400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr13:50296400-50302000	Weak transcription	Thymus	Thymus
43	chr13:50296400-50307200	Weak transcription	Psoas Muscle	Psoas
44	chr13:50296400-50307600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr13:50296400-50320200	Weak transcription	Spleen	Spleen
46	chr13:50296600-50300400	Weak transcription	Left Ventricle	heart
47	chr13:50296600-50300400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr13:50296600-50302200	Weak transcription	K562	blood
49	chr13:50296600-50305800	Weak transcription	A549	lung
50	chr13:50296600-50306000	Weak transcription	NHLF	lung

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