Variant report

Variant	rs202551
Chromosome Location	chr20:1659728-1659729
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:1659496-1659734	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000236550	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10211741	0.81[JPT][hapmap]
rs10211807	0.81[JPT][hapmap]
rs1022641	0.88[ASN][1000 genomes]
rs11698603	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs12624984	0.80[ASN][1000 genomes]
rs12625034	0.80[ASN][1000 genomes]
rs12625207	0.80[ASN][1000 genomes]
rs12625431	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs12625449	0.81[JPT][hapmap]
rs12625628	0.80[ASN][1000 genomes]
rs12625665	0.80[ASN][1000 genomes]
rs12626154	0.80[ASN][1000 genomes]
rs1438104	0.80[ASN][1000 genomes]
rs1438105	0.80[ASN][1000 genomes]
rs1438106	0.90[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs1550263	0.80[ASN][1000 genomes]
rs1550264	0.80[ASN][1000 genomes]
rs1550265	0.80[ASN][1000 genomes]
rs1550266	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs1550267	0.80[ASN][1000 genomes]
rs202474	0.80[EUR][1000 genomes]
rs202475	0.80[EUR][1000 genomes]
rs202493	0.85[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs202513	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs202516	0.85[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs202517	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs202519	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs202528	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs202533	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs202534	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs202538	0.80[ASN][1000 genomes]
rs202539	0.80[ASN][1000 genomes]
rs202540	0.80[ASN][1000 genomes]
rs202541	0.80[ASN][1000 genomes]
rs202542	0.80[ASN][1000 genomes]
rs202543	0.80[ASN][1000 genomes]
rs202544	0.80[ASN][1000 genomes]
rs202545	0.80[ASN][1000 genomes]
rs202546	0.80[ASN][1000 genomes]
rs202547	0.80[ASN][1000 genomes]
rs202549	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202550	0.80[ASN][1000 genomes]
rs202552	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs202554	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250253	0.80[ASN][1000 genomes]
rs2318047	0.81[JPT][hapmap]
rs3761271	0.81[JPT][hapmap]
rs4254564	0.91[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs4254565	0.80[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs4254566	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs4353709	0.91[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs4413221	0.80[ASN][1000 genomes]
rs4473456	0.91[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs498139	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs515883	0.84[CHB][hapmap]
rs517578	0.85[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap]
rs572620	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs577238	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs57724095	0.80[ASN][1000 genomes]
rs578970	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs599837	0.85[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap]
rs600303	0.85[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap]
rs6034307	0.81[JPT][hapmap]
rs6034359	0.80[ASN][1000 genomes]
rs6034368	0.91[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs6034370	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs6034371	0.80[ASN][1000 genomes]
rs6034372	0.80[ASN][1000 genomes]
rs6043506	0.81[JPT][hapmap]
rs6043688	0.80[ASN][1000 genomes]
rs6043713	0.80[ASN][1000 genomes]
rs6043714	0.80[ASN][1000 genomes]
rs6043722	0.91[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs6043726	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs60824122	0.80[ASN][1000 genomes]
rs6110760	0.81[JPT][hapmap]
rs72484090	0.80[ASN][1000 genomes]
rs72484093	0.80[ASN][1000 genomes]
rs7263011	0.81[JPT][hapmap]
rs7275082	0.80[ASN][1000 genomes]
rs73085061	0.80[ASN][1000 genomes]
rs7345130	0.80[ASN][1000 genomes]
rs761824	0.88[ASN][1000 genomes]
rs963168	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv1063015	chr20:1531131-1674430	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	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
11	esv3454857	chr20:1545594-1674850	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	esv3454856	chr20:1545691-1674811	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	esv3454858	chr20:1545691-1674811	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs202551	SCRT2	cis	cerebellum	SCAN
rs202551	SRXN1	cis	cerebellum	SCAN
rs202551	HSPA12B	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1646200-1660200	Enhancers	Primary T cells fromperipheralblood	blood
2	chr20:1655600-1662200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr20:1655800-1660200	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr20:1655800-1660400	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr20:1656000-1659800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr20:1658000-1663600	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr20:1658200-1661000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr20:1658200-1662200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr20:1658200-1664600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr20:1658400-1661800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr20:1659200-1659800	Enhancers	Primary T cells from cord blood	blood
12	chr20:1659400-1660200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr20:1659600-1659800	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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