Variant report

Variant	rs1041795
Chromosome Location	chr21:39852396-39852397
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:39848201..39851847-chr21:39852141..39856874,4	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12481801	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs13051739	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2212933	1.00[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2836424	0.94[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2836429	0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs2836435	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836436	0.82[MEX][hapmap]
rs3787903	0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs3787909	0.83[JPT][hapmap]
rs7282099	0.89[ASN][1000 genomes]
rs9977083	0.94[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9978004	0.80[CHB][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059340	chr21:39817504-39881353	Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1064436	chr21:39846571-39875576	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1041795	PCP4	cis	parietal	SCAN
rs1041795	KCNE2	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:39843400-39855200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr21:39843400-39858200	Weak transcription	Esophagus	oesophagus
3	chr21:39846400-39855600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr21:39846400-39855800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr21:39847400-39852400	Enhancers	Left Ventricle	heart
6	chr21:39848400-39858600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr21:39849200-39852800	Enhancers	HMEC	breast
8	chr21:39849600-39852800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr21:39849600-39858600	Enhancers	Primary hematopoietic stem cells	blood
10	chr21:39850000-39852400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr21:39850000-39852600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr21:39850400-39858200	Weak transcription	Right Atrium	heart
13	chr21:39850600-39854800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr21:39851000-39853600	Weak transcription	Fetal Heart	heart
15	chr21:39851000-39853800	Weak transcription	Adipose Nuclei	Adipose
16	chr21:39851200-39856000	Weak transcription	NH-A	brain
17	chr21:39852000-39852400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr21:39852000-39852400	Enhancers	Aorta	Aorta
19	chr21:39852000-39852800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr21:39852000-39853200	Enhancers	NHEK	skin
21	chr21:39852000-39856400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr21:39852200-39853600	Enhancers	HUVEC	blood vessel
23	chr21:39852200-39858000	Weak transcription	Lung	lung
24	chr21:39852200-39858800	Weak transcription	Fetal Thymus	thymus
25	chr21:39852200-39860000	Weak transcription	Spleen	Spleen

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