Variant report

Variant	rs2209313
Chromosome Location	chr20:1599142-1599143
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1061179	0.88[ASN][1000 genomes]
rs11696739	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11696842	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11697985	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12480515	0.81[CHB][hapmap]
rs1535882	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2243423	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2243603	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap]
rs2246154	0.87[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap]
rs2249317	0.87[CHB][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap]
rs2250199	0.87[CHB][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.85[YRI][hapmap]
rs2253427	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs2254194	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap]
rs2254448	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap]
rs2256520	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2263664	0.94[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap]
rs2317869	0.90[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap]
rs2317870	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2318043	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422615	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs2422631	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs2746607	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap]
rs2746608	0.90[CEU][hapmap];0.88[JPT][hapmap]
rs2746609	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2873569	0.82[ASW][hapmap];0.90[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap]
rs2982585	0.86[CHD][hapmap];0.88[JPT][hapmap]
rs34600126	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761268	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761269	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[ASN][1000 genomes]
rs3848784	0.86[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap]
rs3848786	0.81[CHB][hapmap]
rs3848787	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs3848788	0.87[CHB][hapmap];0.90[CHD][hapmap]
rs6034006	0.87[CHB][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap]
rs6034039	0.81[CHB][hapmap]
rs6074894	0.98[ASN][1000 genomes]
rs6079527	0.81[CHB][hapmap]
rs6079867	0.99[ASN][1000 genomes]
rs6079882	0.89[ASN][1000 genomes]
rs6105334	0.81[CHB][hapmap]
rs6110353	0.81[CHB][hapmap]
rs67499412	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:44 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv510779	chr20:1509330-1613962	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	esv1814180	chr20:1540847-1601747	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	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
15	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
16	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
17	nsv3253	chr20:1547092-1603832	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv965840	chr20:1551250-1601116	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv184	chr20:1551392-1599647	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv821006	chr20:1551643-1601157	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv828665	chr20:1551643-1601157	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
22	esv1806656	chr20:1553470-1651867	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
23	nsv1058480	chr20:1560240-1599142	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv1056222	chr20:1560531-1599142	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
25	nsv1064545	chr20:1560775-1599142	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
26	nsv1056058	chr20:1560775-1599572	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
27	nsv1058817	chr20:1560910-1599142	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
28	nsv1066585	chr20:1560910-1599572	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
29	nsv1061677	chr20:1560939-1599142	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
30	nsv1059046	chr20:1561568-1599142	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
31	nsv1058509	chr20:1561568-1599572	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
32	nsv1063401	chr20:1561641-1599142	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
33	nsv1067325	chr20:1567442-1599142	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
34	nsv1067203	chr20:1567732-1599142	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
35	nsv1067242	chr20:1567994-1599142	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
36	nsv1056496	chr20:1570725-1599142	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
37	nsv1062461	chr20:1570740-1599142	Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
38	nsv1061742	chr20:1571091-1599142	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
39	nsv1060282	chr20:1571366-1599142	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
40	nsv1060899	chr20:1572123-1599142	Genic enhancers Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
41	nsv1057460	chr20:1579109-1599572	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region	2 gene(s)	inside rSNPs	diseases
42	esv3454892	chr20:1585279-1617007	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
43	esv3454893	chr20:1585279-1617007	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
44	nsv965842	chr20:1592092-1599257	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2209313	SIRPB1	cis	Whole Blood	GTEx
rs2209313	RP4-576H24.5	cis	Whole Blood	GTEx
rs2209313	SIRPB1	cis	Nerve Tibial	GTEx
rs2209313	SIRPB1	cis	Thyroid	GTEx
rs2209313	SIRPB1	cis	Artery Tibial	GTEx
rs2209313	DEFB126	cis	parietal	SCAN
rs2209313	C20orf141	cis	parietal	SCAN
rs2209313	C20orf29	cis	cerebellum	SCAN
rs2209313	SIRPB1	cis	lung	GTEx
rs2209313	SIRPB1	cis	Adipose Subcutaneous	GTEx
rs2209313	PTPNS1L2	cis	multi-tissue	Pritchard
rs2209313	WTIP	trans	cerebellum	SCAN
rs2209313	SIRPB1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1570400-1599800	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr20:1589600-1600000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr20:1592400-1599200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr20:1596400-1602400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr20:1596600-1599400	Enhancers	HUVEC	blood vessel
6	chr20:1597400-1599600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr20:1598000-1600200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr20:1598400-1600600	Weak transcription	Hela-S3	cervix
9	chr20:1598800-1599800	ZNF genes & repeats	Primary B cells from cord blood	blood
10	chr20:1598800-1600000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
11	chr20:1598800-1600200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr20:1598800-1600800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
13	chr20:1598800-1601800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr20:1599000-1599400	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr20:1599000-1600000	ZNF genes & repeats	Primary T cells from cord blood	blood
16	chr20:1599000-1601800	Enhancers	Spleen	Spleen

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