Variant report

Variant	rs2054977
Chromosome Location	chr5:68553646-68553647
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68548010..68550361-chr5:68553101..68555711,2	K562	blood:
2	chr5:68514852..68516852-chr5:68553089..68555836,2	K562	blood:
3	chr5:68549479..68552120-chr5:68553320..68555643,3	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10940206	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12651858	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12652124	0.81[ASN][1000 genomes]
rs12656423	0.97[EUR][1000 genomes]
rs12656449	0.97[EUR][1000 genomes]
rs12656918	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12657418	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069433	0.80[ASN][1000 genomes]
rs3934529	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4443380	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4976158	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59515371	0.97[EUR][1000 genomes]
rs60113639	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60824482	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73125214	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73125295	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73127319	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73127323	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73127331	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7733529	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1795469	chr5:68534233-68565285	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2054977	CCDC125	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68531200-68584200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:68531400-68605000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:68531600-68554600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:68531800-68554600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr5:68531800-68556000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr5:68531800-68556800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:68532400-68558600	Weak transcription	Brain Substantia Nigra	brain
8	chr5:68532400-68558800	Weak transcription	Brain Angular Gyrus	brain
9	chr5:68532400-68563600	Weak transcription	Fetal Brain Male	brain
10	chr5:68532400-68574600	Weak transcription	Spleen	Spleen
11	chr5:68533200-68576800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr5:68534400-68554600	Weak transcription	Gastric	stomach
13	chr5:68534400-68556000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr5:68534400-68575200	Weak transcription	Aorta	Aorta
15	chr5:68534800-68554200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:68535200-68558800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr5:68535200-68559400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr5:68535400-68556600	Weak transcription	HSMMtube	muscle
19	chr5:68538400-68563600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:68539000-68559200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr5:68539200-68554600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr5:68541200-68620400	Weak transcription	Stomach Mucosa	stomach
23	chr5:68544600-68554600	Weak transcription	Brain Germinal Matrix	brain
24	chr5:68546200-68560600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:68546200-68562200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:68546200-68579200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr5:68546400-68556200	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:68546400-68569000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr5:68546600-68566600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr5:68546800-68555800	Weak transcription	Pancreas	Pancrea
31	chr5:68547600-68556600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:68548400-68557200	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr5:68548400-68560600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr5:68548600-68566600	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr5:68548800-68562000	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr5:68549400-68565000	Weak transcription	Small Intestine	intestine
37	chr5:68549400-68577600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:68549600-68577600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:68549800-68567800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr5:68550200-68555600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr5:68550400-68560200	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr5:68550400-68581800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr5:68550600-68559800	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr5:68550600-68561000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr5:68550600-68562800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:68550600-68577000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:68550800-68554200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:68550800-68556600	Strong transcription	Osteobl	bone
49	chr5:68550800-68560400	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr5:68550800-68560400	Strong transcription	Primary T helper cells fromperipheralblood	blood

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