Variant report

Variant	rs517578
Chromosome Location	chr20:1689270-1689271
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	MAFK	chr20:1689002-1689324	IMR90	lung:	n/a	n/a
2	GATA1	chr20:1688515-1689453	PBDE	blood:	n/a	chr20:1688916-1688923 chr20:1688916-1688926 chr20:1689125-1689138 chr20:1688911-1688927 chr20:1689127-1689135 chr20:1688905-1688922 chr20:1688911-1688927 chr20:1688916-1688923 chr20:1688916-1688923
3	SPI1	chr20:1689259-1689736	HL-60	blood:	n/a	chr20:1689487-1689494

Variant related genes	Relation type
SIRPB3P	TF binding region

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs12625431	0.80[CHB][hapmap]
rs1438106	0.81[CHB][hapmap]
rs1550265	0.89[CHB][hapmap]
rs1550266	0.81[CHB][hapmap]
rs169354	0.98[ASN][1000 genomes]
rs202461	0.85[EUR][1000 genomes]
rs202462	0.84[EUR][1000 genomes]
rs202463	0.85[EUR][1000 genomes]
rs202464	0.98[ASN][1000 genomes]
rs202465	0.98[ASN][1000 genomes]
rs202467	0.85[EUR][1000 genomes]
rs202472	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs202474	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs202475	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs202476	0.94[ASN][1000 genomes]
rs202477	0.92[ASN][1000 genomes]
rs202493	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.98[ASN][1000 genomes]
rs202494	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202495	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202496	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202497	0.98[ASN][1000 genomes]
rs202498	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202499	0.98[ASN][1000 genomes]
rs202500	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202501	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202502	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202503	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202504	0.96[ASN][1000 genomes]
rs202505	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202506	0.97[ASN][1000 genomes]
rs202507	0.84[EUR][1000 genomes]
rs202508	0.84[EUR][1000 genomes]
rs202509	0.84[EUR][1000 genomes]
rs202510	0.85[EUR][1000 genomes]
rs202511	0.98[ASN][1000 genomes]
rs202512	0.98[ASN][1000 genomes]
rs202513	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs202514	0.82[CEU][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs202515	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs202516	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.98[ASN][1000 genomes]
rs202517	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs202518	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs202519	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs202551	0.85[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap]
rs202552	0.80[CHB][hapmap]
rs2247997	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4254564	0.81[CHB][hapmap]
rs4254566	0.80[CHB][hapmap]
rs4353709	0.81[CHB][hapmap]
rs4473456	0.81[CHB][hapmap]
rs480743	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480769	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482716	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493466	1.00[ASN][1000 genomes]
rs497134	0.94[ASN][1000 genomes]
rs498139	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs513119	1.00[ASN][1000 genomes]
rs513201	1.00[ASN][1000 genomes]
rs514813	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514965	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs515973	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs528256	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532097	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544110	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549733	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs572620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577238	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs578127	1.00[ASN][1000 genomes]
rs578970	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs585046	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs588555	0.90[ASN][1000 genomes]
rs599837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600303	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs601652	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6034368	0.81[CHB][hapmap]
rs6034370	0.80[CHB][hapmap]
rs6043722	0.81[CHB][hapmap]
rs6043726	0.80[CHB][hapmap]
rs615007	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629812	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629867	1.00[ASN][1000 genomes]
rs629878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648051	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs659348	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs679310	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692847	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs692891	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	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
5	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
6	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
7	nsv1063429	chr20:1679052-1706969	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1793674	chr20:1685595-1704114	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs517578	SRXN1	cis	cerebellum	SCAN
rs517578	NSFL1C	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1688000-1689600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr20:1688200-1689400	Enhancers	Primary B cells from cord blood	blood
3	chr20:1688200-1689400	Enhancers	Primary T cells fromperipheralblood	blood
4	chr20:1688200-1689400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr20:1688200-1689400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr20:1688200-1689600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr20:1688200-1689600	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr20:1688200-1689600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr20:1688200-1689800	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr20:1688200-1689800	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr20:1688200-1689800	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr20:1688200-1690000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr20:1688200-1690000	Enhancers	Fetal Thymus	thymus
14	chr20:1688200-1690200	Enhancers	Primary hematopoietic stem cells	blood
15	chr20:1688200-1690200	Enhancers	Thymus	Thymus
16	chr20:1688400-1689600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr20:1688600-1689400	Enhancers	GM12878-XiMat	blood
18	chr20:1688600-1689600	Enhancers	K562	blood
19	chr20:1688800-1689600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr20:1688800-1693000	Weak transcription	HMEC	breast
21	chr20:1689200-1689600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
22	chr20:1689200-1689600	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr20:1689200-1690200	Enhancers	Primary T cells from cord blood	blood

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