Variant report

Variant	rs2306119
Chromosome Location	chr1:226420722-226420723
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10753418	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs10799340	0.87[MEX][hapmap]
rs12136759	0.87[MEX][hapmap]
rs1219652	0.85[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes]
rs1219659	1.00[CEU][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1361559	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs2199501	0.82[AMR][1000 genomes]
rs2927339	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3008189	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3008190	0.96[CEU][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3008191	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3008192	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6668540	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6703375	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7367845	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7368170	0.94[ASW][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.95[LWK][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs9286999	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs9629826	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9728663	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9728665	0.86[AMR][1000 genomes];0.83[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2306119	ACBD3	cis	normal skin	skin_eQTL
rs2306119	ACBD3	Cis_1M	lymphoblastoid	RTeQTL
rs2306119	PARP1	cis	cerebellum	SCAN
rs2306119	JMJD4	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226412000-226424200	Weak transcription	Psoas Muscle	Psoas
2	chr1:226412000-226426200	Weak transcription	Lung	lung
3	chr1:226412000-226427600	Weak transcription	Spleen	Spleen
4	chr1:226412000-226428000	Weak transcription	Pancreas	Pancrea
5	chr1:226412000-226429400	Weak transcription	Gastric	stomach
6	chr1:226412000-226431200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:226412000-226449600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:226412000-226455400	Weak transcription	Ovary	ovary
9	chr1:226412000-226456200	Weak transcription	NH-A	brain
10	chr1:226412000-226460600	Weak transcription	Aorta	Aorta
11	chr1:226412200-226424000	Weak transcription	NHEK	skin
12	chr1:226412200-226424400	Weak transcription	A549	lung
13	chr1:226412200-226424400	Weak transcription	HMEC	breast
14	chr1:226412200-226425800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:226412200-226426000	Weak transcription	Brain Substantia Nigra	brain
16	chr1:226412200-226428000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:226412200-226437200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:226412200-226448000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:226412200-226456200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:226412200-226485400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:226412400-226424400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:226412400-226435600	Weak transcription	Hela-S3	cervix
23	chr1:226412400-226442600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:226412400-226443000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:226412400-226443000	Weak transcription	Osteobl	bone
26	chr1:226412400-226446800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:226412800-226421000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:226413000-226445000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:226413000-226448600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:226413200-226424400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr1:226413200-226456200	Weak transcription	NHDF-Ad	bronchial
32	chr1:226413600-226424400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:226413600-226429200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr1:226413600-226440600	Weak transcription	Thymus	Thymus
35	chr1:226413600-226447000	Weak transcription	Brain Germinal Matrix	brain
36	chr1:226413600-226447800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:226413800-226423200	Weak transcription	Fetal Lung	lung
38	chr1:226413800-226424400	Weak transcription	Fetal Intestine Small	intestine
39	chr1:226414000-226424200	Weak transcription	Fetal Brain Female	brain
40	chr1:226414000-226424400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:226414000-226428600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr1:226414000-226436600	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:226414000-226456800	Weak transcription	Fetal Kidney	kidney
44	chr1:226414200-226421000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr1:226414200-226424400	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr1:226414200-226447200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr1:226414200-226454400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:226414400-226423600	Weak transcription	Fetal Brain Male	brain
49	chr1:226414600-226457000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:226414800-226421000	Weak transcription	GM12878-XiMat	blood

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