Variant report

Variant	rs58001045
Chromosome Location	chr15:39746207-39746208
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39744731..39747916-chr15:39873044..39877161,3	MCF-7	breast:
2	chr15:39739352..39742846-chr15:39745277..39748876,4	MCF-7	breast:
3	chr15:39743414..39749749-chr15:39871400..39878085,10	MCF-7	breast:
4	chr15:39745636..39749475-chr15:39752031..39754404,4	K562	blood:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs58836677	1.00[AMR][1000 genomes]
rs59550930	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59611156	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59752089	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60077096	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60658485	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60729119	1.00[AMR][1000 genomes]
rs60772140	1.00[AMR][1000 genomes]
rs60780722	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61052847	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61140941	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61294562	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61583976	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73393465	1.00[AMR][1000 genomes]
rs73393501	1.00[AMR][1000 genomes]
rs73395320	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73395324	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73395336	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73395338	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73395340	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73397317	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73397334	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73397367	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8028168	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1042824	chr15:39676039-39757222	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv542362	chr15:39676039-39757222	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1052908	chr15:39692049-39750193	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1044082	chr15:39693241-39750193	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1036091	chr15:39699841-39750193	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	esv3419623	chr15:39742460-39746758	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv3310891	chr15:39743285-39746233	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv569224	chr15:39744272-39748158	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv511556	chr15:39744272-39748389	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv569226	chr15:39744425-39748158	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39727200-39746800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr15:39740000-39759400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr15:39740400-39747200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:39744000-39747600	Weak transcription	NHLF	lung
5	chr15:39744400-39748400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr15:39744600-39753400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:39745200-39746600	Enhancers	Fetal Stomach	stomach
8	chr15:39745200-39747400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:39745400-39746800	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr15:39745400-39746800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr15:39745400-39747400	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr15:39745400-39747800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr15:39745400-39748800	Enhancers	Osteobl	bone
14	chr15:39745400-39749600	Enhancers	Fetal Lung	lung
15	chr15:39745600-39746600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:39745600-39747600	Enhancers	HepG2	liver
17	chr15:39745600-39748200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:39745600-39748400	Weak transcription	Colon Smooth Muscle	Colon
19	chr15:39745600-39748400	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr15:39745600-39748600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr15:39745600-39748800	Enhancers	NHDF-Ad	bronchial
22	chr15:39745600-39749000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:39745800-39749400	Enhancers	Adipose Nuclei	Adipose
24	chr15:39745800-39749600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:39746000-39746400	Enhancers	GM12878-XiMat	blood
26	chr15:39746000-39746400	Weak transcription	K562	blood
27	chr15:39746000-39748000	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr15:39746000-39748600	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:39746200-39747400	Weak transcription	NH-A	brain
30	chr15:39746200-39747600	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links