Variant report

Variant	rs13214191
Chromosome Location	chr6:44340937-44340938
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10948134	0.94[CEU][hapmap]
rs16871772	0.94[CEU][hapmap]
rs2221224	0.94[CEU][hapmap]
rs4711780	0.84[CEU][hapmap]
rs4714782	0.94[CEU][hapmap]
rs4714783	0.84[CEU][hapmap]
rs4714784	0.94[CEU][hapmap]
rs4714785	0.94[CEU][hapmap]
rs6911823	0.84[CEU][hapmap]
rs6918742	0.81[EUR][1000 genomes]
rs7772720	0.84[CEU][hapmap]
rs883193	0.84[CEU][hapmap]
rs9349283	0.86[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9395009	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9395010	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9395011	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9472263	0.94[CEU][hapmap]
rs950230	0.94[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv1019145	chr6:44313576-44421440	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1794353	chr6:44333489-44350716	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13214191	PEX6	cis	cerebellum	SCAN
rs13214191	CCND3	cis	parietal	SCAN
rs13214191	MED20	cis	parietal	SCAN
rs13214191	SLC25A27	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44335800-44342400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:44340400-44341000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:44340400-44341200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr6:44340400-44341200	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr6:44340400-44341800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:44340400-44342000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:44340400-44342000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:44340400-44342400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:44340400-44343000	Enhancers	HMEC	breast
10	chr6:44340400-44343000	Enhancers	NHEK	skin
11	chr6:44340600-44341000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr6:44340600-44341000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr6:44340600-44341000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:44340600-44341800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr6:44340800-44341000	Enhancers	Liver	Liver

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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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