Variant report

Variant	rs17769580
Chromosome Location	chr2:46896893-46896894
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CRIPT-1	chr2:46896009-46897917	NONHSAT070521

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10495937	0.85[EUR][1000 genomes]
rs1446496	0.80[EUR][1000 genomes]
rs1446497	0.80[EUR][1000 genomes]
rs1446498	0.80[EUR][1000 genomes]
rs1563406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17035429	0.88[EUR][1000 genomes]
rs17035437	0.88[EUR][1000 genomes]
rs17035438	0.88[EUR][1000 genomes]
rs17769041	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17769689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17769921	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17771005	0.89[CEU][hapmap]
rs17771017	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17771942	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17772285	0.80[EUR][1000 genomes]
rs17820969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17821218	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17821989	0.80[EUR][1000 genomes]
rs17822782	0.80[EUR][1000 genomes]
rs17823065	0.80[CEU][hapmap]
rs17823581	0.80[CEU][hapmap]
rs2045290	0.80[EUR][1000 genomes]
rs2124472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3927078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41379148	0.80[EUR][1000 genomes]
rs55775748	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56199036	0.80[EUR][1000 genomes]
rs56800355	0.80[EUR][1000 genomes]
rs58903656	0.80[EUR][1000 genomes]
rs6731970	0.86[CEU][hapmap]
rs6732079	0.88[EUR][1000 genomes]
rs6735101	1.00[CEU][hapmap]
rs72800570	0.88[EUR][1000 genomes]
rs72800576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72800577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72800587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72800597	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72800599	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72800600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72800602	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72802404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72802406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72802407	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72802408	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs72802411	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs72802412	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72802415	0.83[EUR][1000 genomes]
rs72802420	0.80[EUR][1000 genomes]
rs72802426	0.80[EUR][1000 genomes]
rs72802444	0.80[EUR][1000 genomes]
rs72802448	0.80[EUR][1000 genomes]
rs72802451	0.80[EUR][1000 genomes]
rs72802454	0.80[EUR][1000 genomes]
rs72802455	0.80[EUR][1000 genomes]
rs72802456	0.80[EUR][1000 genomes]
rs72802466	0.80[EUR][1000 genomes]
rs72802467	0.80[EUR][1000 genomes]
rs72802486	0.80[EUR][1000 genomes]
rs72802487	0.80[EUR][1000 genomes]
rs7566275	1.00[CEU][hapmap];0.83[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:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46889600-46898200	Enhancers	Fetal Stomach	stomach
2	chr2:46890400-46897000	Enhancers	Rectal Smooth Muscle	rectum
3	chr2:46891400-46898400	Weak transcription	Psoas Muscle	Psoas
4	chr2:46892800-46898400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:46893000-46898200	Enhancers	NHDF-Ad	bronchial
6	chr2:46893400-46897200	Weak transcription	Fetal Heart	heart
7	chr2:46894400-46897200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:46895000-46897400	Weak transcription	Fetal Brain Male	brain
9	chr2:46895800-46897000	Weak transcription	A549	lung
10	chr2:46895800-46898600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:46896200-46897400	Enhancers	Fetal Muscle Trunk	muscle
12	chr2:46896200-46897600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:46896400-46898000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:46896400-46899200	Enhancers	NHLF	lung
15	chr2:46896600-46897000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:46896600-46897200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:46896600-46898200	Enhancers	HSMMtube	muscle
18	chr2:46896800-46898000	Enhancers	NH-A	brain
19	chr2:46896800-46901200	Weak transcription	Fetal Muscle Leg	muscle

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