Variant report

Variant	rs2046850
Chromosome Location	chr1:210304319-210304320
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10863810	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11119399	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11119421	0.85[AMR][1000 genomes]
rs11119422	0.83[AMR][1000 genomes]
rs11119423	0.80[AMR][1000 genomes]
rs12029138	0.87[AMR][1000 genomes]
rs12130989	0.84[AMR][1000 genomes]
rs12739243	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2046851	0.93[ASN][1000 genomes]
rs4271216	0.85[AMR][1000 genomes]
rs4537554	0.85[AMR][1000 genomes]
rs4609425	0.87[AMR][1000 genomes]
rs7516843	0.83[AMR][1000 genomes]
rs7527845	0.83[AMR][1000 genomes]
rs7535045	0.87[AMR][1000 genomes]
rs7536761	0.93[AMR][1000 genomes]
rs7545279	0.93[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv873140	chr1:210068117-210335644	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv873144	chr1:210252522-210347417	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv818800	chr1:210258653-210304319	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv873145	chr1:210302595-210347417	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv468072	chr1:210304319-210338196	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv549104	chr1:210304319-210338196	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv549105	chr1:210304319-210338397	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2046850	SLC30A1	cis	cerebellum	SCAN
rs2046850	SYT14	cis	parietal	SCAN
rs2046850	IL24	cis	cerebellum	SCAN
rs2046850	PFKFB2	cis	cerebellum	SCAN
rs2046850	FCAMR	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210298400-210318200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:210299600-210305800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:210303200-210305200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:210303400-210308200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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