Variant report

Variant	rs2126573
Chromosome Location	chr1:226444946-226444947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10127753	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10127776	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10127970	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10753416	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10799341	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10799343	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10799344	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10799346	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10799347	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10915962	0.82[EUR][1000 genomes]
rs10915964	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10915970	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1219658	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1417766	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1813323	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2126577	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2126578	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2169567	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2254723	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2377026	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2377028	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2377029	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2615799	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2615803	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2666429	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2889537	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2927338	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4418563	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4612598	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6605032	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7552015	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9725097	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9729447	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv2829936	chr1:226375267-226488826	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv517107	chr1:226375267-226508645	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv873233	chr1:226385623-226508645	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2126573	ACBD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226412000-226449600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:226412000-226455400	Weak transcription	Ovary	ovary
3	chr1:226412000-226456200	Weak transcription	NH-A	brain
4	chr1:226412000-226460600	Weak transcription	Aorta	Aorta
5	chr1:226412200-226448000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:226412200-226456200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:226412200-226485400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:226412400-226446800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:226413000-226445000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:226413000-226448600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:226413200-226456200	Weak transcription	NHDF-Ad	bronchial
12	chr1:226413600-226447000	Weak transcription	Brain Germinal Matrix	brain
13	chr1:226413600-226447800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:226414000-226456800	Weak transcription	Fetal Kidney	kidney
15	chr1:226414200-226447200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:226414200-226454400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:226414600-226457000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:226414800-226484600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:226415400-226473800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:226415600-226450000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:226415800-226495400	Weak transcription	Liver	Liver
22	chr1:226416200-226495600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:226416400-226457400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:226418400-226455400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:226418400-226484600	Weak transcription	Right Ventricle	heart
26	chr1:226421800-226457400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr1:226422800-226445000	Weak transcription	NHLF	lung
28	chr1:226424400-226449800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr1:226425000-226452200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:226425000-226456200	Weak transcription	HMEC	breast
31	chr1:226425000-226456600	Weak transcription	NHEK	skin
32	chr1:226425000-226474200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:226425600-226447800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:226426200-226446800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:226426200-226449000	Weak transcription	Fetal Brain Female	brain
36	chr1:226426600-226445400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:226426800-226447800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:226427000-226447800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:226427000-226450200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:226427800-226448000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr1:226432800-226452400	Weak transcription	Fetal Intestine Large	intestine
42	chr1:226433000-226450200	Weak transcription	A549	lung
43	chr1:226434200-226496000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:226436400-226447000	Weak transcription	GM12878-XiMat	blood
45	chr1:226436600-226447000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr1:226436800-226496000	Weak transcription	Esophagus	oesophagus
47	chr1:226437000-226447600	Weak transcription	Fetal Lung	lung
48	chr1:226437400-226455200	Weak transcription	Hela-S3	cervix
49	chr1:226437600-226445600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:226438200-226447800	Weak transcription	Fetal Heart	heart

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