Variant report

Variant	rs6553781
Chromosome Location	chr4:175246203-175246204
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10520278	1.00[JPT][hapmap]
rs10520279	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs13122347	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs13137178	0.95[JPT][hapmap]
rs1472872	0.90[ASN][1000 genomes]
rs17060428	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs17060454	1.00[JPT][hapmap]
rs57241669	0.91[ASN][1000 genomes]
rs7671444	0.95[JPT][hapmap]
rs906569	1.00[JPT][hapmap]
rs906570	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016910	chr4:174952788-175349057	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537363	chr4:174952788-175349057	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv596234	chr4:175053051-175361437	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv869116	chr4:175231090-175801761	Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6553781	KIAA1712	cis	parietal	SCAN
rs6553781	KIAA1712	cis	cerebellum	SCAN
rs6553781	FBXO8	cis	parietal	SCAN
rs6553781	FBXO8	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175214600-175254800	Weak transcription	Esophagus	oesophagus
2	chr4:175232400-175247000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:175233800-175252600	Weak transcription	Left Ventricle	heart
4	chr4:175233800-175255800	Weak transcription	Fetal Intestine Large	intestine
5	chr4:175236200-175258400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:175238000-175254800	Weak transcription	Adipose Nuclei	Adipose
7	chr4:175238000-175255400	Weak transcription	Primary B cells from cord blood	blood
8	chr4:175239200-175253600	Weak transcription	NHEK	skin
9	chr4:175239400-175248400	Weak transcription	Primary T cells from cord blood	blood
10	chr4:175241400-175257400	Weak transcription	Fetal Thymus	thymus
11	chr4:175242200-175252400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr4:175242400-175253000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:175245400-175246400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr4:175245400-175246400	Enhancers	K562	blood
15	chr4:175245400-175246800	Enhancers	HSMM	muscle
16	chr4:175245600-175246400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:175245800-175246400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:175246200-175246400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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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