Variant report

Variant	rs6933965
Chromosome Location	chr6:38895358-38895359
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1929900	1.00[CEU][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3734612	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs4714200	1.00[CEU][hapmap]
rs6458087	0.91[ASW][hapmap];1.00[CEU][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6905467	0.91[ASW][hapmap];1.00[CEU][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6928176	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6933584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6940724	0.91[ASW][hapmap];1.00[CEU][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs7357080	0.83[ASW][hapmap];0.82[TSI][hapmap]
rs7752004	0.82[TSI][hapmap]
rs862438	0.91[CEU][hapmap];0.84[TSI][hapmap]
rs9296268	0.91[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs9369091	0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv830643	chr6:38726675-38905589	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv885821	chr6:38843970-39039503	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv462918	chr6:38875752-38901236	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv602961	chr6:38875752-38901236	Enhancers Weak transcription Flanking Active TSS	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
rs6933965	CLPS	cis	cerebellum	SCAN
rs6933965	LRFN2	cis	cerebellum	SCAN
rs6933965	GUCA1B	cis	cerebellum	SCAN
rs6933965	TMEM129	trans	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38889000-38895400	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr6:38893400-38895400	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr6:38894800-38896200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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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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