Variant report

Variant	rs1002670
Chromosome Location	chr2:40520082-40520083
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs41537645	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs4645043	1.00[ASW][hapmap]
rs7601140	1.00[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv34071	chr2:40435231-40578229	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1002670	TPM2	trans	lymphoblastoid	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40512400-40526200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:40512800-40530000	Weak transcription	NHDF-Ad	bronchial
3	chr2:40515200-40527600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:40515200-40531400	Weak transcription	Osteobl	bone
5	chr2:40515400-40520200	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:40515800-40530400	Weak transcription	Right Ventricle	heart
7	chr2:40517000-40526000	Weak transcription	Left Ventricle	heart
8	chr2:40517400-40520600	Enhancers	Fetal Heart	heart
9	chr2:40517400-40526000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:40518200-40540600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr2:40518400-40526000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr2:40519400-40520200	Enhancers	Fetal Stomach	stomach
13	chr2:40519600-40520400	Enhancers	Rectal Smooth Muscle	rectum
14	chr2:40519800-40527400	Weak transcription	HSMM	muscle
15	chr2:40520000-40520200	Enhancers	Brain Anterior Caudate	brain
16	chr2:40520000-40520400	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr2:40520000-40520800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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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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