Variant report

Variant	rs1561315
Chromosome Location	chr2:178559408-178559409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178557827..178560384-chr2:178566181..178567818,2	K562	blood:
2	chr2:178559293..178562880-chr2:178620510..178622541,4	K562	blood:
3	chr2:178553724..178556122-chr2:178557669..178561053,4	K562	blood:
4	chr2:178557613..178559704-chr2:178561778..178563487,2	K562	blood:

Variant related genes	Relation type
ENSG00000229941	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1004541	0.88[ASN][1000 genomes]
rs1004542	0.88[ASN][1000 genomes]
rs10192481	0.86[ASN][1000 genomes]
rs10201180	0.88[ASN][1000 genomes]
rs10930805	0.88[ASN][1000 genomes]
rs11677821	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1347731	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1370662	0.88[ASN][1000 genomes]
rs1370663	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1370664	0.88[ASN][1000 genomes]
rs1438054	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1438055	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1469972	0.88[ASN][1000 genomes]
rs1469973	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs16865645	0.81[EUR][1000 genomes]
rs1975321	0.88[ASN][1000 genomes]
rs1975322	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2033760	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2164860	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2886424	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3731809	0.88[ASN][1000 genomes]
rs3770023	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4893980	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4893981	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893982	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893984	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893985	0.88[ASN][1000 genomes]
rs6718702	0.88[ASN][1000 genomes]
rs6760930	0.88[ASN][1000 genomes]
rs7596360	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs934809	0.88[ASN][1000 genomes]
rs999218	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases
3	nsv431812	chr2:178525371-178584470	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1007925	chr2:178535922-178577002	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv870023	chr2:178545623-178581407	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1005854	chr2:178546907-178586608	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv2762967	chr2:178546919-178577002	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1005991	chr2:178550049-178577002	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv528219	chr2:178551924-178567151	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1003983	chr2:178551958-178577002	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178555400-178559800	Enhancers	Fetal Kidney	kidney
2	chr2:178557400-178560200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:178558200-178576600	Weak transcription	Pancreas	Pancrea
4	chr2:178558400-178560800	Weak transcription	HepG2	liver
5	chr2:178558600-178562000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:178559000-178563600	Weak transcription	Ovary	ovary
7	chr2:178559200-178561200	Weak transcription	Liver	Liver
8	chr2:178559200-178561600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links