Variant report

Variant	rs4886574
Chromosome Location	chr15:74461720-74461721
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:74460105-74471859	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:74449618..74451381-chr15:74459821..74462700,2	K562	blood:
2	chr15:74461480..74463993-chr15:74464056..74467832,4	MCF-7	breast:

Variant related genes	Relation type
ISLR	TF binding region
ENSG00000129009	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1052622	0.86[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10910	0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1385650	0.83[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs351237	0.88[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs351238	0.83[CEU][hapmap]
rs351243	0.91[ASN][1000 genomes]
rs4887066	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6495089	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758387	chr15:74215114-74464916	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv2760040	chr15:74215114-74464916	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv428308	chr15:74215114-74464916	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv469619	chr15:74291859-74466321	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv482362	chr15:74291859-74466321	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv833053	chr15:74360156-74555140	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1050884	chr15:74394983-74489413	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv904345	chr15:74458181-74526596	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv904346	chr15:74458181-74548773	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4886574	C15orf39	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74449400-74465600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:74450600-74462400	Weak transcription	Fetal Brain Male	brain
3	chr15:74460000-74462600	Enhancers	Fetal Heart	heart
4	chr15:74460000-74465600	Enhancers	Fetal Muscle Leg	muscle
5	chr15:74460200-74463800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr15:74460200-74465600	Enhancers	Ovary	ovary
7	chr15:74460200-74466000	Enhancers	Fetal Muscle Trunk	muscle
8	chr15:74460200-74466000	Enhancers	Fetal Stomach	stomach
9	chr15:74460200-74466400	Enhancers	Spleen	Spleen
10	chr15:74460400-74462000	Enhancers	Right Atrium	heart
11	chr15:74460400-74462200	Enhancers	Left Ventricle	heart
12	chr15:74460400-74462200	Enhancers	Right Ventricle	heart
13	chr15:74460400-74463400	Enhancers	Stomach Smooth Muscle	stomach
14	chr15:74460600-74461800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:74460600-74461800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:74460600-74463000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:74460600-74464600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:74460800-74462000	Enhancers	Adipose Nuclei	Adipose
19	chr15:74460800-74462000	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr15:74460800-74462000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr15:74460800-74462400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr15:74460800-74462600	Enhancers	Colon Smooth Muscle	Colon
23	chr15:74461000-74462800	Weak transcription	GM12878-XiMat	blood
24	chr15:74461000-74463400	Weak transcription	Lung	lung
25	chr15:74461000-74465600	Enhancers	Fetal Lung	lung
26	chr15:74461000-74465600	Enhancers	Placenta	Placenta
27	chr15:74461200-74462000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
28	chr15:74461400-74464800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:74461400-74465000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:74461400-74465200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:74461600-74461800	Enhancers	Fetal Kidney	kidney
32	chr15:74461600-74464800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr15:74461600-74465200	Weak transcription	HSMMtube	muscle
34	chr15:74461600-74466200	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links