Variant report

Variant	rs62454876
Chromosome Location	chr7:27663840-27663841
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10486549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11550134	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12667470	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1524525	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17155498	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17155501	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17155505	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17155525	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17155537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2192559	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2391450	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34905189	0.82[EUR][1000 genomes]
rs58231871	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58857361	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59686784	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61407744	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62454870	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62454871	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62454872	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62454908	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62454914	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62456947	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62456951	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6947004	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72596952	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72596966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs759268	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7778454	0.80[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	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv1802647	chr7:27658495-27673924	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62454876	TAX1BP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27651800-27674200	Weak transcription	Hela-S3	cervix
2	chr7:27654400-27696400	Weak transcription	Gastric	stomach
3	chr7:27655400-27665200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr7:27658800-27687800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:27658800-27688600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:27659800-27672800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr7:27659800-27675400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr7:27659800-27679000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:27660000-27664400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:27660000-27667600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr7:27660000-27669800	Weak transcription	Left Ventricle	heart
12	chr7:27660000-27680600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr7:27660200-27668000	Weak transcription	Osteobl	bone
14	chr7:27660200-27674600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr7:27660400-27668600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:27660400-27675600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:27660400-27680200	Weak transcription	Fetal Kidney	kidney
18	chr7:27660600-27666600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr7:27660600-27667800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr7:27660600-27674800	Weak transcription	Psoas Muscle	Psoas
21	chr7:27660600-27701000	Weak transcription	Right Ventricle	heart
22	chr7:27660800-27668400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr7:27660800-27675600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr7:27660800-27676400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr7:27661000-27666000	Weak transcription	Placenta	Placenta
26	chr7:27661000-27666000	Weak transcription	A549	lung
27	chr7:27661000-27666400	Weak transcription	Adipose Nuclei	Adipose
28	chr7:27661000-27666600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr7:27661000-27666600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr7:27661000-27666600	Weak transcription	HSMM	muscle
31	chr7:27661000-27667400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:27661000-27675000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr7:27661000-27675400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr7:27661000-27679600	Weak transcription	HSMMtube	muscle
35	chr7:27661000-27680600	Weak transcription	HepG2	liver
36	chr7:27661000-27688000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr7:27661200-27667800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr7:27661200-27675200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr7:27661200-27694800	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr7:27661400-27666600	Weak transcription	Liver	Liver
41	chr7:27661400-27668600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr7:27661400-27669800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr7:27661400-27670000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr7:27661400-27675200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr7:27661400-27688800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr7:27661400-27700800	Weak transcription	Thymus	Thymus
47	chr7:27661600-27668000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr7:27661600-27681000	Weak transcription	NHEK	skin
49	chr7:27661800-27666600	Weak transcription	Ovary	ovary
50	chr7:27661800-27669800	Weak transcription	Fetal Stomach	stomach

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