Variant report

Variant	rs2273329
Chromosome Location	chr20:1678188-1678189
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10211741	0.80[JPT][hapmap]
rs10211807	0.81[JPT][hapmap]
rs11698603	0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11698636	0.89[ASN][1000 genomes]
rs12624984	0.90[ASN][1000 genomes]
rs12625034	0.90[ASN][1000 genomes]
rs12625207	0.90[ASN][1000 genomes]
rs12625431	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs12625449	0.81[JPT][hapmap]
rs12625628	0.90[ASN][1000 genomes]
rs12625665	0.90[ASN][1000 genomes]
rs12626154	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1438104	0.90[ASN][1000 genomes]
rs1438105	0.90[ASN][1000 genomes]
rs1438106	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs1550263	0.90[ASN][1000 genomes]
rs1550264	0.90[ASN][1000 genomes]
rs1550265	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs1550266	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs1550267	0.90[ASN][1000 genomes]
rs202493	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs202513	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs202516	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs202517	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs202519	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs202537	0.86[ASN][1000 genomes]
rs202538	0.90[ASN][1000 genomes]
rs202539	0.90[ASN][1000 genomes]
rs202540	0.90[ASN][1000 genomes]
rs202541	0.90[ASN][1000 genomes]
rs202542	0.90[ASN][1000 genomes]
rs202543	0.90[ASN][1000 genomes]
rs202544	0.90[ASN][1000 genomes]
rs202545	0.90[ASN][1000 genomes]
rs202546	0.90[ASN][1000 genomes]
rs202547	0.90[ASN][1000 genomes]
rs202550	0.90[ASN][1000 genomes]
rs202551	0.81[CHD][hapmap];0.91[JPT][hapmap]
rs202552	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs202553	0.88[ASN][1000 genomes]
rs2250253	0.90[ASN][1000 genomes]
rs2318047	0.81[JPT][hapmap]
rs3761271	0.81[JPT][hapmap]
rs4254564	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.84[MKK][hapmap];0.90[ASN][1000 genomes]
rs4254565	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs4254566	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs4353709	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.84[MKK][hapmap];0.90[ASN][1000 genomes]
rs4413221	0.90[ASN][1000 genomes]
rs4473456	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs498139	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs515883	0.81[JPT][hapmap]
rs517578	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs56113269	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs572620	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs577238	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs57724095	0.90[ASN][1000 genomes]
rs578970	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs599837	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs600303	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6034307	0.81[JPT][hapmap]
rs6034356	0.89[ASN][1000 genomes]
rs6034359	0.90[ASN][1000 genomes]
rs6034368	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs6034370	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs6034371	0.90[ASN][1000 genomes]
rs6034372	0.90[ASN][1000 genomes]
rs6043403	0.81[JPT][hapmap]
rs6043506	0.81[JPT][hapmap]
rs6043688	0.90[ASN][1000 genomes]
rs6043713	0.90[ASN][1000 genomes]
rs6043714	0.90[ASN][1000 genomes]
rs6043722	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6043726	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs60733085	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60824122	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6110760	0.81[JPT][hapmap]
rs6110828	0.81[ASN][1000 genomes]
rs6110845	0.84[ASN][1000 genomes]
rs6110853	0.84[ASN][1000 genomes]
rs72484089	0.84[ASN][1000 genomes]
rs72484090	0.90[ASN][1000 genomes]
rs72484092	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72484093	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7263011	0.81[JPT][hapmap]
rs7275082	0.90[ASN][1000 genomes]
rs73085061	0.90[ASN][1000 genomes]
rs7345130	0.90[ASN][1000 genomes]
rs73604189	0.80[ASN][1000 genomes]
rs963168	0.81[JPT][hapmap]
rs968860	0.84[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2273329	SRXN1	cis	cerebellum	SCAN

Chromatin state (count:13 , 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

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