Variant report

Variant	rs62454870
Chromosome Location	chr7:27650526-27650527
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	chr7:27646394..27648572-chr7:27650317..27653232,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10486549	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11550134	0.86[AMR][1000 genomes]
rs12667470	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12670250	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13242238	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13245339	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1524525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17155498	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17155501	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17155505	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17155525	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17155537	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2192559	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2391450	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34536886	0.80[ASN][1000 genomes]
rs34905189	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58231871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59686784	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61407744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62454871	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62454872	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62454876	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62454908	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62454914	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62456947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62456951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6947004	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72596952	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72596966	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs759268	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62454870	TAX1BP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27582400-27650800	Weak transcription	Left Ventricle	heart
2	chr7:27609400-27651000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:27615600-27657800	Weak transcription	Aorta	Aorta
4	chr7:27616000-27650800	Weak transcription	Fetal Kidney	kidney
5	chr7:27626600-27654800	Weak transcription	Placenta	Placenta
6	chr7:27626800-27655800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:27628200-27658400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr7:27628600-27658400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr7:27629600-27655400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:27630200-27654600	Weak transcription	Primary B cells from cord blood	blood
11	chr7:27630400-27656800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr7:27632200-27655600	Weak transcription	Primary T cells from cord blood	blood
13	chr7:27644200-27655400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr7:27644400-27658400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr7:27645400-27655600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr7:27646000-27655200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:27646200-27651800	Enhancers	Hela-S3	cervix
18	chr7:27646200-27655600	Weak transcription	Fetal Muscle Leg	muscle
19	chr7:27646200-27657800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr7:27646400-27650800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:27646400-27650800	Weak transcription	NHDF-Ad	bronchial
22	chr7:27646400-27654800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:27646400-27655600	Weak transcription	Fetal Stomach	stomach
24	chr7:27646600-27656600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr7:27646600-27658400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr7:27646800-27655600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr7:27646800-27657800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:27646800-27658800	Weak transcription	Osteobl	bone
29	chr7:27646800-27659600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr7:27647000-27655800	Weak transcription	Ovary	ovary
31	chr7:27647000-27657200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:27647000-27660200	Weak transcription	Small Intestine	intestine
33	chr7:27647200-27650800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr7:27647200-27655600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr7:27647200-27655600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr7:27648600-27650800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr7:27648600-27655600	Weak transcription	HepG2	liver
38	chr7:27648600-27659800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr7:27648800-27657800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr7:27648800-27658200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr7:27648800-27658200	Weak transcription	HSMMtube	muscle
42	chr7:27649000-27650800	Weak transcription	Liver	Liver
43	chr7:27649000-27651000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr7:27649000-27655800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr7:27649000-27658400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr7:27649200-27650600	Weak transcription	HSMM	muscle
47	chr7:27649200-27650600	Weak transcription	NHEK	skin
48	chr7:27649200-27650800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr7:27649200-27655000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:27649200-27655400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links