Variant report

Variant	rs2025345
Chromosome Location	chr10:6067688-6067689
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11256457	0.87[CEU][hapmap];0.80[AMR][1000 genomes]
rs12358961	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4749926	0.90[CHB][hapmap]
rs6602392	0.80[CHB][hapmap]
rs7072398	0.90[CHB][hapmap]
rs9663421	0.83[ASW][hapmap]

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	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv525927	chr10:6059898-6078079	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Self-reported allergy	23817569	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2025345	PITRM1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6057400-6068600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr10:6057800-6069600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr10:6057800-6069800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr10:6058000-6068600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr10:6059400-6068800	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr10:6060400-6070000	Weak transcription	Lung	lung
7	chr10:6060800-6075800	Weak transcription	Colon Smooth Muscle	Colon
8	chr10:6061200-6070000	Weak transcription	Spleen	Spleen
9	chr10:6062800-6067800	Strong transcription	Primary B cells from peripheral blood	blood
10	chr10:6063000-6068400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr10:6066600-6079600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr10:6066800-6069200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr10:6066800-6069200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr10:6066800-6078000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr10:6067000-6069600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr10:6067000-6070000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr10:6067400-6069400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr10:6067600-6068200	Genic enhancers	Pancreatic Islets	Pancreatic Islet
19	chr10:6067600-6068400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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