Variant report

Variant	rs1563406
Chromosome Location	chr2:46893332-46893333
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46891488..46894291-chr2:46897484..46899463,3	K562	blood:
2	chr2:46891705..46893482-chr2:46919094..46921446,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10495937	0.83[EUR][1000 genomes]
rs17035429	0.87[EUR][1000 genomes]
rs17035437	0.87[EUR][1000 genomes]
rs17035438	0.87[EUR][1000 genomes]
rs17769041	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17769580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17769689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17769921	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17771017	0.80[CEU][hapmap]
rs17820969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17821218	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2124472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3927078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55775748	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6732079	0.87[EUR][1000 genomes]
rs72800570	0.87[EUR][1000 genomes]
rs72800576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72800577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72800587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72800597	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72800599	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72800600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72800602	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72802404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72802406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72802407	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72802408	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs72802411	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs72802412	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs72802415	0.82[EUR][1000 genomes]
rs7566275	0.80[CEU][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
7	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46884400-46896400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:46889000-46896800	Enhancers	Fetal Muscle Leg	muscle
3	chr2:46889200-46896400	Enhancers	Colon Smooth Muscle	Colon
4	chr2:46889600-46898200	Enhancers	Fetal Stomach	stomach
5	chr2:46890200-46896400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:46890400-46894400	Weak transcription	Aorta	Aorta
7	chr2:46890400-46897000	Enhancers	Rectal Smooth Muscle	rectum
8	chr2:46891200-46895800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:46891200-46896400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:46891200-46896600	Weak transcription	HSMMtube	muscle
11	chr2:46891400-46893400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:46891400-46898400	Weak transcription	Psoas Muscle	Psoas
13	chr2:46891600-46893400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:46891600-46893400	Weak transcription	Right Atrium	heart
15	chr2:46891600-46896400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:46891800-46894600	Enhancers	Stomach Smooth Muscle	stomach
17	chr2:46891800-46895000	Weak transcription	Right Ventricle	heart
18	chr2:46891800-46896400	Weak transcription	Left Ventricle	heart
19	chr2:46892000-46895400	Enhancers	Fetal Lung	lung
20	chr2:46892000-46896000	Enhancers	Ovary	ovary
21	chr2:46892600-46894600	Enhancers	Fetal Muscle Trunk	muscle
22	chr2:46892800-46898400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:46893000-46893400	Enhancers	Fetal Heart	heart
24	chr2:46893000-46898200	Enhancers	NHDF-Ad	bronchial
25	chr2:46893200-46893400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:46893200-46893400	Enhancers	Fetal Brain Female	brain
27	chr2:46893200-46893600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:46893200-46894400	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr2:46893200-46894600	Enhancers	Adipose Nuclei	Adipose
30	chr2:46893200-46894600	Enhancers	Fetal Kidney	kidney
31	chr2:46893200-46894600	Enhancers	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links