Variant report

Variant	rs4239709
Chromosome Location	chr20:1383729-1383730
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11087049	0.98[ASN][1000 genomes]
rs12626072	0.98[ASN][1000 genomes]
rs2092877	0.96[ASN][1000 genomes]
rs2092878	0.94[ASN][1000 genomes]
rs2092879	0.91[ASN][1000 genomes]
rs2092880	0.89[ASN][1000 genomes]
rs2317648	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4814222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814223	1.00[ASN][1000 genomes]
rs4814224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56377442	0.89[ASN][1000 genomes]
rs6033645	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6033666	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033673	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6033674	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6033677	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6033678	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6041880	0.85[JPT][hapmap]
rs6041970	0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6041971	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6041976	0.92[ASN][1000 genomes]
rs6042009	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042018	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6042021	0.94[ASN][1000 genomes]
rs6042022	0.96[ASN][1000 genomes]
rs6042024	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6042026	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6109813	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6134845	0.97[ASN][1000 genomes]
rs6134846	0.97[ASN][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	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	esv3454734	chr20:1380804-1384028	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv3454733	chr20:1380917-1383913	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3454735	chr20:1380931-1383912	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4239709	NSFL1C	cis	multi-tissue	Pritchard
rs4239709	SPEF1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1378600-1384400	Enhancers	Fetal Intestine Small	intestine
2	chr20:1379600-1383800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr20:1380000-1384400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:1380600-1383800	Enhancers	NHEK	skin
5	chr20:1380600-1388400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr20:1381800-1383800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr20:1382400-1386000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr20:1382400-1388400	Weak transcription	Placenta	Placenta
9	chr20:1382800-1383800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr20:1382800-1383800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr20:1382800-1383800	Enhancers	Dnd41	blood
12	chr20:1383000-1383800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr20:1383200-1388000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr20:1383400-1383800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr20:1383400-1384200	Weak transcription	HMEC	breast
16	chr20:1383600-1385600	Weak transcription	Fetal Intestine Large	intestine

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