Variant report

Variant	rs2722175
Chromosome Location	chr12:104435587-104435588
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12427086	0.94[ASN][1000 genomes]
rs12581921	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs1564892	0.90[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs17035129	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17035153	0.85[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2583230	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2629751	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2629798	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2722170	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2723867	0.88[ASN][1000 genomes]
rs55675238	0.87[ASN][1000 genomes]
rs55997300	0.87[ASN][1000 genomes]
rs56269347	0.90[ASN][1000 genomes]
rs57041861	0.97[ASN][1000 genomes]
rs7358625	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2722175	CHST11	cis	parietal	SCAN
rs2722175	GLT8D2	cis	parietal	SCAN
rs2722175	TCP11L2	cis	cerebellum	SCAN
rs2722175	ARL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104408800-104442200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:104424800-104438800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:104428400-104439000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:104429200-104438400	Weak transcription	Colon Smooth Muscle	Colon
5	chr12:104429600-104438800	Weak transcription	Ovary	ovary
6	chr12:104432600-104435600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:104432800-104439000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:104434400-104435600	Weak transcription	Fetal Stomach	stomach
9	chr12:104435000-104442000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:104435200-104435600	Strong transcription	Fetal Muscle Leg	muscle
11	chr12:104435200-104435800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:104435200-104436000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:104435200-104436000	Strong transcription	Fetal Muscle Trunk	muscle
14	chr12:104435200-104436600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:104435400-104438800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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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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