Variant report

Variant	rs2520343
Chromosome Location	chr7:18843808-18843809
allele	A/C
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]
rs10245511	0.83[EUR][1000 genomes]
rs10251998	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10269422	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12699984	0.92[ASN][1000 genomes]
rs13246896	1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[ASN][1000 genomes]
rs2520341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2520342	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2520354	0.89[CHB][hapmap];0.89[CHD][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2520355	0.87[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2588621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2588635	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[ASN][1000 genomes]
rs2588637	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2588638	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6965278	0.93[ASN][1000 genomes]
rs7459007	0.87[ASN][1000 genomes]
rs7794273	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7810384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv498112	chr7:18677922-18991946	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv887813	chr7:18720135-18995552	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv887814	chr7:18751998-18886177	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	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
rs2520343	SLC12A6	trans	lymphoblastoid	seeQTL
rs2520343	AGR3	cis	parietal	SCAN
rs2520343	AHR	cis	cerebellum	SCAN
rs2520343	ABLIM1	trans	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:18834200-18845200	Weak transcription	Aorta	Aorta
2	chr7:18838600-18845600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr7:18843400-18844000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr7:18843400-18844200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:18843600-18844000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:18843600-18844000	Enhancers	HMEC	breast
7	chr7:18843600-18844400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:18843600-18845200	Enhancers	Fetal Heart	heart
9	chr7:18843800-18844000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:18843800-18844200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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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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