Variant report

Variant	rs2873569
Chromosome Location	chr20:1585838-1585839
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 306 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11696739	0.86[CHD][hapmap];0.88[JPT][hapmap]
rs11696842	0.81[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs11697985	0.90[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs1535882	0.86[CHD][hapmap];0.88[JPT][hapmap]
rs2209313	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]
rs2243423	0.87[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap]
rs2243603	1.00[ASW][hapmap];0.90[CEU][hapmap];0.87[CHB][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap]
rs2246154	1.00[YRI][hapmap]
rs2249317	0.83[LWK][hapmap]
rs2250199	0.83[LWK][hapmap];1.00[YRI][hapmap]
rs2253427	1.00[ASW][hapmap];0.90[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs2254194	0.90[CEU][hapmap];0.87[CHB][hapmap]
rs2254448	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap]
rs2263664	0.87[CHB][hapmap];0.83[LWK][hapmap]
rs2317869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2317870	0.90[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap]
rs2422615	0.87[CHB][hapmap]
rs2422631	0.90[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap]
rs2746607	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2746608	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2746609	0.86[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap]
rs2982585	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs3761268	0.81[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs3761269	0.88[JPT][hapmap]
rs3848784	1.00[YRI][hapmap]
rs3848787	0.87[CHB][hapmap]
rs3848788	0.81[CHB][hapmap]
rs6034006	0.83[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:278 , 50 per page) page: 1 2 3 4 5 6

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	nsv1055446	chr20:1546750-1597934	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	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
19	esv2760679	chr20:1550334-1599078	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
20	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
21	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
22	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
23	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
24	esv1810126	chr20:1552088-1597566	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
25	esv1809194	chr20:1552094-1592383	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
26	esv1816104	chr20:1552094-1592383	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
27	nsv1063461	chr20:1552104-1593837	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
28	esv2763670	chr20:1552116-1598336	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
29	esv11812	chr20:1552338-1596222	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
30	esv1814643	chr20:1552415-1592383	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
31	esv1817470	chr20:1552415-1592383	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
32	nsv1060586	chr20:1552430-1593837	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
33	esv1823021	chr20:1553470-1597566	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
34	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
35	esv1818900	chr20:1554154-1594982	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
36	esv3445130	chr20:1554782-1587897	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
37	nsv498959	chr20:1555755-1589375	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
38	nsv1057099	chr20:1557178-1593837	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
39	esv2421429	chr20:1557190-1593893	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
40	esv3453902	chr20:1559252-1586450	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
41	nsv1062375	chr20:1559700-1593837	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
42	esv3523272	chr20:1559852-1595500	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
43	nsv512601	chr20:1559975-1596077	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
44	esv3453901	chr20:1559977-1587325	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
45	esv3453903	chr20:1559977-1587325	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
46	esv3373524	chr20:1560052-1587800	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
47	esv2556331	chr20:1560150-1594595	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
48	nsv1062582	chr20:1560240-1590522	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
49	nsv1059849	chr20:1560240-1593837	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
50	nsv1066579	chr20:1560240-1597934	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2873569	DEFB126	cis	parietal	SCAN
rs2873569	STK35	cis	parietal	SCAN
rs2873569	WTIP	trans	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1569800-1587000	Weak transcription	Spleen	Spleen
2	chr20:1570400-1599800	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr20:1571000-1599000	Weak transcription	Primary T cells from cord blood	blood
4	chr20:1580000-1591400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr20:1584200-1590200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr20:1585000-1590000	Weak transcription	Primary neutrophils fromperipheralblood	blood

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