Variant report

Variant	rs16888420
Chromosome Location	chr6:57121359-57121360
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	chr6:57117734..57121990-chr6:57123203..57126438,5	MCF-7	breast:
2	chr6:57117930..57121391-chr6:57123083..57125355,3	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10080526	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10949013	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs10949014	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs16888410	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16888435	0.95[ASN][1000 genomes]
rs16888439	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs223289	0.83[CHB][hapmap]
rs62415953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62415955	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62415956	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62418081	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62418083	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6900622	0.81[ASN][1000 genomes]
rs6905598	0.81[ASN][1000 genomes]
rs6906645	0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs6918565	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9357941	1.00[TSI][hapmap]
rs9396263	1.00[TSI][hapmap]
rs9475804	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9475805	0.86[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs9475808	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs984684	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats 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 miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1034095	chr6:57102042-57162808	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv528165	chr6:57104266-57130574	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:57118200-57122400	Weak transcription	NH-A	brain
2	chr6:57118400-57122200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr6:57118400-57122400	Weak transcription	Aorta	Aorta
4	chr6:57118400-57122400	Weak transcription	HSMMtube	muscle
5	chr6:57118400-57126600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr6:57118400-57128200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:57118800-57121400	Weak transcription	Osteobl	bone
8	chr6:57118800-57121600	Weak transcription	NHLF	lung
9	chr6:57118800-57122800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr6:57119000-57121600	Weak transcription	NHDF-Ad	bronchial
11	chr6:57119000-57122200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:57119000-57122400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:57119200-57121400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:57119200-57122400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:57119200-57122400	Weak transcription	Ovary	ovary
16	chr6:57119400-57121400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:57119400-57121400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:57119400-57122200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:57119400-57122400	Weak transcription	Fetal Stomach	stomach
20	chr6:57119600-57122400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr6:57120400-57122600	Enhancers	Colon Smooth Muscle	Colon
22	chr6:57120800-57122400	Enhancers	Rectal Smooth Muscle	rectum
23	chr6:57121000-57122000	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr6:57121000-57122400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:57121200-57122400	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links