Variant report

Variant	rs6817835
Chromosome Location	chr4:124547636-124547637
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10518419	0.98[ASN][1000 genomes]
rs11723511	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11730924	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11946918	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12504496	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510059	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs13124203	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2553382	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2553383	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589857	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71608146	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv469710	chr4:124474286-124623722	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv482747	chr4:124474286-124623722	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv830047	chr4:124504051-124699142	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv879873	chr4:124528452-124590869	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6817835	PKD1L1	trans	cerebellum	SCAN
rs6817835	NUDT6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:124543200-124552800	Weak transcription	Adipose Nuclei	Adipose
2	chr4:124545600-124549600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:124547600-124548000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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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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