Variant report

Variant	rs2207831
Chromosome Location	chr20:1402213-1402214
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs2224148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6074603	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6074608	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6074609	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6074625	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079018	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6079040	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6079044	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6079045	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6079053	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6079055	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6079082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62186872	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62186873	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7270038	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7271175	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7353854	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv432095	chr20:1382500-1420340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2207831	NSFL1C	cis	cerebellum	SCAN
rs2207831	SIRPB2	cis	parietal	SCAN
rs2207831	SIRPG	cis	lymphoblastoid	seeQTL
rs2207831	NSFL1C	cis	multi-tissue	Pritchard
rs2207831	SOX12	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1399400-1403200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr20:1399800-1404400	Weak transcription	NHLF	lung
3	chr20:1399800-1415000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr20:1400000-1403200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr20:1400000-1404200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr20:1400000-1408200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr20:1400000-1410600	Weak transcription	Osteobl	bone
8	chr20:1400600-1403600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr20:1401600-1402600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr20:1401800-1404400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr20:1401800-1404600	Enhancers	Placenta	Placenta

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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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