Variant report

Variant	rs1411904
Chromosome Location	chr6:44318072-44318073
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10948132	0.83[CEU][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs1122627	0.83[CHB][hapmap]
rs1411903	0.80[EUR][1000 genomes]
rs1909887	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs2065361	0.83[CHB][hapmap];0.85[CHD][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs6935721	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7769100	0.83[CHB][hapmap];0.83[CHD][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs7769128	0.91[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9462982	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9472259	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472261	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1411904	PEX6	cis	cerebellum	SCAN
rs1411904	CD2AP	cis	cerebellum	SCAN
rs1411904	RRP36	cis	cerebellum	SCAN
rs1411904	MED20	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44317400-44318600	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr6:44317600-44318200	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr6:44317600-44318200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:44317600-44318200	Enhancers	HMEC	breast
5	chr6:44317600-44318400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:44317600-44318600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr6:44317600-44318600	Enhancers	Liver	Liver
8	chr6:44317800-44318200	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr6:44317800-44318200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:44317800-44318400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr6:44317800-44318400	Enhancers	H1 Cell Line	embryonic stem cell
12	chr6:44317800-44318600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr6:44317800-44318600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr6:44317800-44318600	Enhancers	HepG2	liver
15	chr6:44318000-44318400	Enhancers	HUES64 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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