Variant report

Variant	rs16842397
Chromosome Location	chr1:162006015-162006016
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr1:162005711-162007342	SK-N-SH	brain:	n/a	chr1:162007028-162007035 chr1:162006909-162006923
2	RAD21	chr1:162005759-162007370	SK-N-SH	brain:	n/a	chr1:162006914-162006923 chr1:162006905-162006924

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:161999968..162002848-chr1:162004092..162006515,2	K562	blood:
2	chr1:161999968..162003243-chr1:162004092..162006054,3	K562	blood:

Variant related genes	Relation type
ENSG00000227818	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1123217	1.00[CEU][hapmap]
rs17454327	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60340472	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6666546	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74127517	1.00[AMR][1000 genomes];1.00[EUR][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	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv464206	chr1:161798239-162067447	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv470744	chr1:161798239-162067447	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv548077	chr1:161798239-162067447	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv831747	chr1:161926367-162103311	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:162000400-162006400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:162004000-162006200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:162004000-162006400	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:162004600-162006400	Enhancers	Hela-S3	cervix
5	chr1:162004800-162006400	Enhancers	HMEC	breast
6	chr1:162004800-162007200	Enhancers	NHEK	skin
7	chr1:162004800-162007400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:162005000-162006400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:162005000-162006600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:162005000-162006600	Enhancers	NHDF-Ad	bronchial
11	chr1:162005200-162006200	Enhancers	NH-A	brain
12	chr1:162005200-162006400	Enhancers	NHLF	lung
13	chr1:162005200-162006400	Enhancers	Osteobl	bone
14	chr1:162005200-162006600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:162005200-162006600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:162005200-162006800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:162005400-162006400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:162005400-162007000	Weak transcription	Psoas Muscle	Psoas
19	chr1:162005400-162008000	Enhancers	HepG2	liver
20	chr1:162005600-162006200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr1:162005600-162007000	Weak transcription	Right Atrium	heart
22	chr1:162005600-162010200	Weak transcription	Aorta	Aorta

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