Variant report

Variant	rs16987282
Chromosome Location	chr2:20202738-20202739
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1030900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12611974	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12614643	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12622939	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16987211	0.80[EUR][1000 genomes]
rs16987218	1.00[ASW][hapmap];0.81[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs2293670	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3731664	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3731665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3795965	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55919320	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006404	chr2:20167688-20216509	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1005431	chr2:20174676-20210163	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1011244	chr2:20174676-20216204	Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv932888	chr2:20199931-20202894	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20190400-20207400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:20190600-20211400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:20190800-20205000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr2:20190800-20208400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:20191000-20211200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:20191400-20208000	Weak transcription	A549	lung
7	chr2:20197200-20203000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:20200000-20206800	Weak transcription	HSMMtube	muscle
9	chr2:20200200-20211800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:20201600-20203400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:20201800-20211400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:20201800-20212400	Weak transcription	Gastric	stomach
13	chr2:20202000-20210400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:20202400-20210200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:20202600-20203000	Strong transcription	HepG2	liver

Quick Search:

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

what's new

Quick links