Variant report

Variant	rs16823484
Chromosome Location	chr2:178741538-178741539
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	chr2:178740457..178742889-chr2:178751116..178753576,2	K562	blood:
2	chr2:178736620..178738806-chr2:178741458..178743918,2	K562	blood:

Variant related genes	Relation type
ENSG00000128655	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1347440	0.85[AMR][1000 genomes]
rs1527291	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16865786	0.83[EUR][1000 genomes]
rs16865818	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16865821	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16865846	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16865903	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16865998	0.85[AMR][1000 genomes]
rs16865999	0.85[AMR][1000 genomes]
rs16866003	0.85[AMR][1000 genomes]
rs16866043	0.85[AMR][1000 genomes]
rs16866058	0.85[AMR][1000 genomes]
rs3770053	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821011	0.83[EUR][1000 genomes]
rs41357848	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57019461	0.88[AFR][1000 genomes]
rs57352786	1.00[AFR][1000 genomes]
rs57715307	0.84[AFR][1000 genomes]
rs58297855	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58779934	0.92[AFR][1000 genomes]
rs61339042	1.00[AFR][1000 genomes]
rs61448024	1.00[AFR][1000 genomes]
rs61541689	0.84[AFR][1000 genomes]
rs6708449	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717171	1.00[AFR][1000 genomes]
rs6733229	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750238	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578601	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv533377	chr2:178718801-178963463	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1007579	chr2:178729330-178890946	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3458758	chr2:178740578-178742335	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3458755	chr2:178740868-178742214	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3458757	chr2:178740922-178742182	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3458756	chr2:178740928-178742140	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3458754	chr2:178740928-178742247	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv3458752	chr2:178740989-178742113	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv9888	chr2:178740995-178742118	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv3458759	chr2:178741005-178742108	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178734400-178744800	Weak transcription	Psoas Muscle	Psoas
2	chr2:178736200-178743000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr2:178739200-178743000	Weak transcription	Adipose Nuclei	Adipose
4	chr2:178739400-178744800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:178739600-178741600	Weak transcription	Liver	Liver
6	chr2:178739600-178744800	Weak transcription	HepG2	liver
7	chr2:178740000-178742200	Weak transcription	Fetal Intestine Large	intestine
8	chr2:178740000-178744800	Weak transcription	Fetal Intestine Small	intestine
9	chr2:178741000-178759200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links