Variant report

Variant	rs12040408
Chromosome Location	chr1:85614893-85614894
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85607229..85609639-chr1:85613340..85615534,2	K562	blood:

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1037745	0.90[ASN][1000 genomes]
rs11161533	0.98[ASN][1000 genomes]
rs11805650	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12021868	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12022814	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12023751	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12028707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12034359	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12034501	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12034937	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12036276	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12039804	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12041155	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12043409	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12045141	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12084434	0.97[ASN][1000 genomes]
rs1674179	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17099217	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs17121656	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs17121745	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs17121935	1.00[AFR][1000 genomes]
rs17121978	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs2007508	0.98[ASN][1000 genomes]
rs2068427	0.96[ASN][1000 genomes]
rs2305930	1.00[AFR][1000 genomes]
rs2305931	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs28410552	1.00[AFR][1000 genomes]
rs2994490	0.96[ASN][1000 genomes]
rs3013111	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3209418	0.97[ASN][1000 genomes]
rs3364	0.96[ASN][1000 genomes]
rs41289039	1.00[AFR][1000 genomes]
rs56191061	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57222060	1.00[AFR][1000 genomes]
rs57516443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57530923	0.98[ASN][1000 genomes]
rs58068482	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58246117	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58604582	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58659750	1.00[AFR][1000 genomes]
rs59030463	1.00[AFR][1000 genomes]
rs59248240	1.00[AFR][1000 genomes]
rs60866399	1.00[AFR][1000 genomes]
rs60875782	0.97[ASN][1000 genomes]
rs709785	0.94[ASN][1000 genomes]
rs709787	0.96[ASN][1000 genomes]
rs72482805	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513769	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs817387	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs817395	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs817400	1.00[ASN][1000 genomes]
rs817409	0.94[ASN][1000 genomes]
rs817410	0.97[ASN][1000 genomes]
rs817413	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs817414	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs817416	0.96[ASN][1000 genomes]
rs817418	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs817419	0.96[ASN][1000 genomes]
rs817420	0.96[ASN][1000 genomes]
rs817421	0.96[ASN][1000 genomes]
rs817424	0.96[ASN][1000 genomes]
rs817426	0.96[ASN][1000 genomes]
rs817427	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs817429	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs817430	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs817431	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs817432	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs817433	0.96[ASN][1000 genomes]
rs817435	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs817437	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs817439	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs817440	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs817441	0.96[ASN][1000 genomes]
rs817452	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85603800-85615600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:85603800-85618800	Weak transcription	Gastric	stomach
3	chr1:85603800-85632200	Weak transcription	Fetal Lung	lung
4	chr1:85608600-85655200	Weak transcription	Aorta	Aorta
5	chr1:85608800-85629200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:85610400-85615600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:85610400-85647800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:85610600-85630600	Weak transcription	Fetal Intestine Small	intestine
9	chr1:85611200-85615200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:85611400-85617000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:85611400-85629600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:85612800-85616000	Enhancers	GM12878-XiMat	blood
13	chr1:85613600-85616000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr1:85613800-85615000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:85613800-85615400	Enhancers	NHDF-Ad	bronchial
16	chr1:85613800-85615600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr1:85613800-85615800	Enhancers	H9 Cell Line	embryonic stem cell
18	chr1:85613800-85615800	Enhancers	Osteobl	bone
19	chr1:85613800-85616000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr1:85613800-85616400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:85614000-85617600	Enhancers	Fetal Heart	heart
22	chr1:85614200-85615000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:85614200-85615000	Weak transcription	Right Ventricle	heart
24	chr1:85614200-85615200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:85614200-85615200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:85614200-85615800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:85614200-85615800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr1:85614200-85615800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:85614200-85616000	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr1:85614200-85616000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:85614200-85616000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:85614200-85616400	Enhancers	Left Ventricle	heart
33	chr1:85614400-85615600	Enhancers	NHLF	lung
34	chr1:85614400-85616000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:85614400-85618800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:85614600-85615000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:85614600-85615200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:85614600-85615200	Enhancers	Placenta Amnion	Placenta Amnion
39	chr1:85614800-85615000	Enhancers	NHEK	skin
40	chr1:85614800-85615400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:85614800-85615600	Enhancers	Muscle Satellite Cultured Cells	--
42	chr1:85614800-85615800	Enhancers	Rectal Smooth Muscle	rectum
43	chr1:85614800-85615800	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr1:85614800-85616000	Enhancers	Stomach Smooth Muscle	stomach
45	chr1:85614800-85619000	Weak transcription	Right Atrium	heart

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