Variant report

Variant	rs4759272
Chromosome Location	chr12:57438658-57438659
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57437727..57439233-chr12:57441223..57443598,2	K562	blood:
2	chr12:57435895..57439296-chr12:57441098..57444197,4	MCF-7	breast:
3	chr12:57417198..57419177-chr12:57437192..57440073,2	MCF-7	breast:
4	chr12:57436724..57439244-chr12:57478812..57480694,2	MCF-7	breast:
5	chr12:57430023..57432254-chr12:57436315..57439287,3	K562	blood:
6	chr12:57437279..57438925-chr12:57505012..57506715,2	K562	blood:
7	chr12:57432807..57436296-chr12:57438112..57442005,3	K562	blood:

Variant related genes	Relation type
ENSG00000166888	Chromatin interaction
ENSG00000166866	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1353781	1.00[LWK][hapmap];0.83[MKK][hapmap]
rs4319546	0.83[MKK][hapmap]
rs840161	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899110	chr12:57422934-57472502	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv899111	chr12:57438658-57472502	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4759272	CYP27B1	cis	parietal	SCAN
rs4759272	GALNT6	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57416800-57439400	Strong transcription	Fetal Intestine Small	intestine
2	chr12:57417200-57441200	Weak transcription	Small Intestine	intestine
3	chr12:57419200-57439400	Strong transcription	Duodenum Mucosa	Duodenum
4	chr12:57419800-57439600	Strong transcription	Fetal Intestine Large	intestine
5	chr12:57420000-57440000	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr12:57420400-57471800	Weak transcription	Gastric	stomach
7	chr12:57421800-57441600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:57433600-57440400	Weak transcription	Primary T cells from cord blood	blood
9	chr12:57433600-57440800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:57433800-57440400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr12:57434400-57439200	Strong transcription	Colonic Mucosa	Colon
12	chr12:57434800-57440400	Weak transcription	Stomach Mucosa	stomach
13	chr12:57435400-57439200	Weak transcription	Thymus	Thymus
14	chr12:57435400-57440000	Weak transcription	Fetal Muscle Leg	muscle
15	chr12:57436200-57440200	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:57437000-57471400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:57438000-57439400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:57438000-57440800	Weak transcription	Spleen	Spleen
19	chr12:57438200-57438800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:57438600-57438800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:57438600-57438800	Enhancers	Fetal Thymus	thymus

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