Variant report

Variant	rs12652476
Chromosome Location	chr5:42702501-42702502
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	chr5:42701145..42703654-chr5:42714759..42717038,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10038285	0.89[JPT][hapmap]
rs10038477	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10041130	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10044169	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10061833	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10077296	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10941583	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12654861	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12656017	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12658099	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12658163	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1423655	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16872680	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872694	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872756	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16872762	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16872777	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16872779	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs16872791	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16872824	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872825	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872830	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16872832	1.00[AMR][1000 genomes]
rs17839373	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17839374	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230808	0.94[ASN][1000 genomes]
rs230809	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs230811	0.91[ASN][1000 genomes]
rs2548719	0.89[ASN][1000 genomes]
rs28918068	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28919894	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28919901	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28919903	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28943887	1.00[EUR][1000 genomes]
rs28943888	1.00[EUR][1000 genomes]
rs2910854	0.94[ASN][1000 genomes]
rs2910860	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2910863	0.94[ASN][1000 genomes]
rs2910866	0.94[ASN][1000 genomes]
rs2910878	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2910879	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972752	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972764	0.81[ASN][1000 genomes]
rs2972768	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972769	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972780	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2972782	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972991	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2972995	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973004	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973008	0.89[ASN][1000 genomes]
rs2973009	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2973016	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973019	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973030	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34319505	1.00[EUR][1000 genomes]
rs34382565	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35291899	0.85[ASN][1000 genomes]
rs35389780	1.00[EUR][1000 genomes]
rs35436563	1.00[EUR][1000 genomes]
rs35604733	1.00[ASN][1000 genomes]
rs4146624	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs4242119	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs4273617	0.89[JPT][hapmap]
rs4376276	0.92[ASN][1000 genomes]
rs4547964	0.84[JPT][hapmap]
rs4637559	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4866947	0.82[ASN][1000 genomes]
rs4866948	0.83[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs6179	0.89[JPT][hapmap]
rs6182	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6184	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7703289	0.89[JPT][hapmap]

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	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1031160	chr5:42610090-42843255	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1019696	chr5:42610090-42844191	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1029933	chr5:42611976-42833385	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv537735	chr5:42611976-42833385	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42688400-42722200	Weak transcription	Pancreas	Pancrea
2	chr5:42689800-42703000	Strong transcription	Liver	Liver
3	chr5:42689800-42703400	Strong transcription	Adipose Nuclei	Adipose
4	chr5:42692200-42703000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr5:42692200-42703200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr5:42692200-42703200	Weak transcription	Right Ventricle	heart
7	chr5:42692200-42705600	Weak transcription	Fetal Muscle Leg	muscle
8	chr5:42692400-42705600	Weak transcription	Colon Smooth Muscle	Colon
9	chr5:42692600-42702800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:42697200-42703000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr5:42698000-42718600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr5:42698800-42705600	Weak transcription	Aorta	Aorta
13	chr5:42698800-42718600	Weak transcription	Left Ventricle	heart
14	chr5:42699000-42703000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr5:42699200-42703800	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr5:42700800-42703200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr5:42701000-42703400	Weak transcription	Fetal Intestine Large	intestine
18	chr5:42701200-42703000	Strong transcription	Fetal Lung	lung
19	chr5:42701200-42718800	Weak transcription	Fetal Stomach	stomach
20	chr5:42701600-42702600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:42701600-42718600	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links