Variant report

Variant	rs57352580
Chromosome Location	chr2:9997794-9997795
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1119632	0.87[ASN][1000 genomes]
rs1119633	0.87[ASN][1000 genomes]
rs11887231	0.87[ASN][1000 genomes]
rs13404815	0.87[ASN][1000 genomes]
rs13429581	0.87[ASN][1000 genomes]
rs16867192	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16867203	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2656329	0.87[ASN][1000 genomes]
rs287975	0.87[ASN][1000 genomes]
rs287976	0.87[ASN][1000 genomes]
rs287977	0.87[ASN][1000 genomes]
rs287978	0.87[ASN][1000 genomes]
rs287979	0.87[ASN][1000 genomes]
rs287980	0.87[ASN][1000 genomes]
rs287981	0.87[ASN][1000 genomes]
rs287982	0.87[ASN][1000 genomes]
rs2884174	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56154233	0.87[ASN][1000 genomes]
rs58521916	0.87[ASN][1000 genomes]
rs72780999	0.94[ASN][1000 genomes]
rs72782605	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72782633	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72782634	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72782637	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9973577	0.87[ASN][1000 genomes]
rs9973654	0.87[ASN][1000 genomes]
rs9973905	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013969	chr2:9888703-10023951	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv873629	chr2:9949464-10016627	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
5	nsv873630	chr2:9953949-10030024	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
6	nsv873631	chr2:9975557-10059770	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
7	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv580960	chr2:9993451-10066694	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57352580	TAF1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9984800-9998400	Weak transcription	Pancreas	Pancrea
2	chr2:9985000-10000800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:9986200-9997800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:9987200-10038400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:9987400-10003200	Weak transcription	Stomach Mucosa	stomach
6	chr2:9987600-9998400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:9989000-9997800	Strong transcription	Primary B cells from peripheral blood	blood
8	chr2:9989000-9997800	Strong transcription	HUVEC	blood vessel
9	chr2:9989000-9997800	Strong transcription	NH-A	brain
10	chr2:9989200-9998200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:9989400-9997800	Strong transcription	Fetal Thymus	thymus
12	chr2:9989400-9998200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:9989400-9998400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:9989400-9999200	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr2:9989400-10000600	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr2:9989400-10001000	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr2:9989600-9997800	Strong transcription	Liver	Liver
18	chr2:9989600-9998400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:9989600-9998400	Strong transcription	Adipose Nuclei	Adipose
20	chr2:9989600-9999200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
21	chr2:9989600-9999400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:9989600-10001200	Strong transcription	Osteobl	bone
23	chr2:9989800-9997800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:9989800-9998200	Strong transcription	Duodenum Mucosa	Duodenum
25	chr2:9989800-9999200	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:9990000-9997800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:9990000-9997800	Strong transcription	Placenta	Placenta
28	chr2:9990000-9998000	Strong transcription	Fetal Muscle Trunk	muscle
29	chr2:9990000-9998600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:9990200-9998800	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr2:9990400-10000600	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr2:9990400-10000800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:9990600-9997800	Strong transcription	Fetal Muscle Leg	muscle
34	chr2:9990600-9997800	Strong transcription	HSMMtube	muscle
35	chr2:9990600-9998400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr2:9990600-9998400	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:9990600-9998600	Strong transcription	Brain Anterior Caudate	brain
38	chr2:9990600-9999200	Strong transcription	Left Ventricle	heart
39	chr2:9990600-10000800	Strong transcription	Stomach Smooth Muscle	stomach
40	chr2:9990600-10001600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:9990800-9999000	Strong transcription	Brain Hippocampus Middle	brain
42	chr2:9991000-9998800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:9992000-9998600	Strong transcription	Ovary	ovary
44	chr2:9992000-9999000	Strong transcription	Brain Cingulate Gyrus	brain
45	chr2:9992200-9998200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr2:9993000-10003600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:9993200-9997800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:9993200-10001200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:9993600-9997800	Weak transcription	HMEC	breast
50	chr2:9993600-10007400	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links