Variant report

Variant	rs7274477
Chromosome Location	chr20:1676943-1676944
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs202478	1.00[ASN][1000 genomes]
rs202479	1.00[ASN][1000 genomes]
rs202480	1.00[ASN][1000 genomes]
rs202481	1.00[ASN][1000 genomes]
rs202482	1.00[ASN][1000 genomes]
rs202483	1.00[ASN][1000 genomes]
rs202484	1.00[ASN][1000 genomes]
rs202485	0.93[ASN][1000 genomes]
rs202486	0.87[ASN][1000 genomes]
rs202487	1.00[ASN][1000 genomes]
rs202521	1.00[ASN][1000 genomes]
rs202524	1.00[ASN][1000 genomes]
rs202526	0.87[ASN][1000 genomes]
rs202527	1.00[ASN][1000 genomes]
rs202530	0.96[ASN][1000 genomes]
rs202532	0.96[ASN][1000 genomes]
rs2244191	1.00[ASN][1000 genomes]
rs4813210	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs548666	1.00[ASN][1000 genomes]
rs6110951	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7269065	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7273080	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8124886	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv2758509	chr20:1476781-1679256	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	esv2758777	chr20:1476781-1679256	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv428374	chr20:1476781-1679256	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv912596	chr20:1486637-1877150	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv1057036	chr20:1493425-1869281	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv912597	chr20:1500506-1877150	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv833894	chr20:1519433-1753366	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv531473	chr20:1532476-1864506	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv3255	chr20:1646524-1680522	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv964356	chr20:1674698-1678227	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs7274477	TMEM159	trans	brain	seeQTL
rs7274477	SMC1A	trans	brain	seeQTL
rs7274477	SLC1A6	trans	brain	seeQTL
rs7274477	CBLN1	trans	brain	seeQTL
rs7274477	TSPAN18	trans	brain	seeQTL
rs7274477	LDLRAP1	trans	brain	seeQTL
rs7274477	CBLB	trans	brain	seeQTL
rs7274477	ANKRD28	trans	brain	seeQTL
rs7274477	CRTAM	trans	brain	seeQTL
rs7274477	NRIP2	trans	brain	seeQTL
rs7274477	PKIB	trans	brain	seeQTL
rs7274477	BARHL1	trans	brain	seeQTL
rs7274477	INSM1	trans	brain	seeQTL
rs7274477	C16orf11	trans	brain	seeQTL
rs7274477	CHD7	trans	brain	seeQTL
rs7274477	PLGLB2	trans	brain	seeQTL
rs7274477	EXPH5	trans	brain	seeQTL
rs7274477	EOMES	trans	brain	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1674600-1680000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr20:1676000-1678400	Enhancers	Primary T cells from cord blood	blood
3	chr20:1676200-1678200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr20:1676200-1678400	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr20:1676200-1678400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr20:1676200-1678600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr20:1676400-1678200	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr20:1676400-1678400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr20:1676400-1678400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr20:1676600-1678200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr20:1676600-1678200	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr20:1676600-1678400	Enhancers	Primary T cells fromperipheralblood	blood
13	chr20:1676600-1678400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr20:1676800-1678000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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