Variant report

Variant	rs942030
Chromosome Location	chr13:50253838-50253839
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	chr13:50253326..50254069-chr13:50365169..50365855,3	MCF-7	breast:
2	chr13:50252667..50256255-chr13:50260389..50264756,4	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1570407	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885539	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407797	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61959934	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61959936	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6561551	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7319110	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7325692	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7327024	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737250	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316473	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs942031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526590	0.84[EUR][1000 genomes]
rs9535292	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535296	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535299	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568305	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv541772	chr13:50218255-50264414	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs942030	TRIM13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50231800-50256000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr13:50235600-50259800	Weak transcription	Right Ventricle	heart
3	chr13:50237000-50256600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr13:50237400-50256000	Weak transcription	NH-A	brain
5	chr13:50241000-50264800	Weak transcription	Aorta	Aorta
6	chr13:50241800-50256000	Weak transcription	HMEC	breast
7	chr13:50242000-50254000	Weak transcription	Fetal Brain Female	brain
8	chr13:50242200-50256200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr13:50242200-50260600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr13:50242200-50261000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr13:50242200-50261400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr13:50242200-50264200	Weak transcription	K562	blood
13	chr13:50242200-50264400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr13:50242200-50264400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr13:50242400-50254200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr13:50242400-50256200	Weak transcription	Brain Substantia Nigra	brain
17	chr13:50242400-50260200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr13:50242400-50260400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr13:50242400-50261400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr13:50242400-50261400	Weak transcription	Gastric	stomach
21	chr13:50242400-50262200	Weak transcription	Spleen	Spleen
22	chr13:50242400-50263200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr13:50242400-50263800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr13:50242400-50264000	Weak transcription	Thymus	Thymus
25	chr13:50242400-50264400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr13:50242400-50264400	Weak transcription	Adipose Nuclei	Adipose
27	chr13:50242400-50264400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr13:50242600-50260000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr13:50244200-50256200	Weak transcription	Fetal Kidney	kidney
30	chr13:50244400-50264400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr13:50244600-50255800	Weak transcription	NHDF-Ad	bronchial
32	chr13:50244800-50255600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr13:50245600-50256000	Weak transcription	Osteobl	bone
34	chr13:50245600-50256200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr13:50245800-50255800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr13:50245800-50256400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr13:50245800-50261400	Weak transcription	HUVEC	blood vessel
38	chr13:50246000-50264600	Weak transcription	Left Ventricle	heart
39	chr13:50246200-50261400	Weak transcription	Hela-S3	cervix
40	chr13:50247000-50264400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr13:50247200-50256000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr13:50247800-50254600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr13:50248400-50263600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr13:50248800-50254400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr13:50249400-50263600	Weak transcription	Primary B cells from cord blood	blood
46	chr13:50249800-50255600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr13:50249800-50255800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr13:50249800-50256000	Weak transcription	NHLF	lung
49	chr13:50250200-50260000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr13:50250400-50256000	Weak transcription	GM12878-XiMat	blood

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