Variant report

Variant	rs41537645
Chromosome Location	chr2:40556387-40556388
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:57914240..57916729-chr2:40555798..40557465,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1002670	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7601140	1.00[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
4	nsv1010508	chr2:40526981-40590777	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv535655	chr2:40526981-40590777	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	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
rs41537645	TPM2	trans	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40542400-40559800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:40542800-40556400	Weak transcription	Fetal Stomach	stomach
3	chr2:40543200-40578800	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr2:40545200-40559200	Weak transcription	HSMM	muscle
5	chr2:40549200-40559800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:40549400-40559000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr2:40549400-40565200	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr2:40550400-40560400	Enhancers	Fetal Heart	heart
9	chr2:40552600-40556600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:40552600-40556600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:40552600-40558800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:40552800-40590600	Weak transcription	Fetal Kidney	kidney
13	chr2:40555200-40556600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:40555400-40557000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:40555600-40556600	Enhancers	Right Ventricle	heart
16	chr2:40555600-40557000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:40555600-40560000	Enhancers	Colon Smooth Muscle	Colon
18	chr2:40555600-40560200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr2:40555800-40556400	Enhancers	Primary hematopoietic stem cells	blood
20	chr2:40555800-40557000	Enhancers	Left Ventricle	heart
21	chr2:40555800-40557600	Enhancers	Fetal Intestine Large	intestine
22	chr2:40555800-40559200	Enhancers	Rectal Smooth Muscle	rectum
23	chr2:40556000-40556600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:40556000-40556800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:40556000-40557600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:40556200-40556600	Enhancers	Hela-S3	cervix
27	chr2:40556200-40557000	Enhancers	Right Atrium	heart
28	chr2:40556200-40557200	Enhancers	NHDF-Ad	bronchial
29	chr2:40556200-40558400	Enhancers	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links