Variant report

Variant	rs3131754
Chromosome Location	chr1:58143696-58143697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10789053	0.93[CHB][hapmap]
rs10889060	0.84[CEU][hapmap]
rs12136261	1.00[CHB][hapmap]
rs1524709	0.92[CEU][hapmap]
rs3131770	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs4420112	0.92[CEU][hapmap]
rs4497237	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs4523535	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs4568858	1.00[CHB][hapmap]
rs6587787	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs6658850	0.82[AMR][1000 genomes]
rs6700116	0.85[JPT][hapmap]
rs6701172	1.00[CHB][hapmap]
rs6702155	0.92[CEU][hapmap]
rs72912422	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7527814	0.92[CEU][hapmap]
rs7531119	0.92[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	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv871620	chr1:58127171-58157778	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3131754	AFARP1	trans	parietal	SCAN
rs3131754	JUN	cis	cerebellum	SCAN
rs3131754	GSTM3	trans	lymphoblastoid	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58143600-58144200	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr1:58143600-58144200	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr1:58143600-58144400	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr1:58143600-58144400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
5	chr1:58143600-58144600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:58143600-58144600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
7	chr1:58143600-58145000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell

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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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