Variant report

Variant	rs1535882
Chromosome Location	chr20:1600524-1600525
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1061179	0.86[ASN][1000 genomes]
rs11696739	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11696842	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11697985	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12480515	0.88[CHB][hapmap]
rs2209313	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2243423	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2243603	0.88[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap]
rs2246154	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2249317	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2250199	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2253427	0.88[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs2254194	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs2254448	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs2256520	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2263664	0.88[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2317869	0.88[JPT][hapmap]
rs2317870	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2318043	0.98[ASN][1000 genomes]
rs2422615	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2422631	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs2746607	0.88[JPT][hapmap]
rs2746608	0.88[JPT][hapmap]
rs2746609	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs2873569	0.86[CHD][hapmap];0.88[JPT][hapmap]
rs2982585	0.82[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap]
rs34600126	0.98[ASN][1000 genomes]
rs3761268	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3761269	0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3848784	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs3848786	0.88[CHB][hapmap]
rs3848787	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs3848788	0.94[CHB][hapmap];0.90[CHD][hapmap]
rs6034006	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs6034039	0.88[CHB][hapmap]
rs6074894	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079527	0.88[CHB][hapmap]
rs6079867	0.97[ASN][1000 genomes]
rs6079882	0.87[ASN][1000 genomes]
rs6105334	0.88[CHB][hapmap]
rs6110353	0.88[CHB][hapmap]
rs67499412	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	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
20	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
21	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
22	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
23	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1535882	RSPO4	cis	parietal	SCAN
rs1535882	FAM110A	cis	lymphoblastoid	seeQTL
rs1535882	RP4-576H24.5	cis	Whole Blood	GTEx
rs1535882	DEFB125	cis	parietal	SCAN
rs1535882	SIRPB1	cis	Nerve Tibial	GTEx
rs1535882	SIRPB1	cis	Whole Blood	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1596400-1602400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr20:1598400-1600600	Weak transcription	Hela-S3	cervix
3	chr20:1598800-1600800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
4	chr20:1598800-1601800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr20:1599000-1601800	Enhancers	Spleen	Spleen
6	chr20:1599400-1600600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
7	chr20:1599400-1602200	Weak transcription	HUVEC	blood vessel
8	chr20:1599800-1600600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr20:1599800-1601600	Enhancers	Dnd41	blood
10	chr20:1599800-1601800	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr20:1599800-1604400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr20:1599800-1608200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr20:1600000-1600800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr20:1600000-1600800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr20:1600000-1602000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr20:1600000-1604400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr20:1600000-1604600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr20:1600000-1608600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr20:1600200-1600600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr20:1600200-1600600	Active TSS	Duodenum Mucosa	Duodenum
21	chr20:1600200-1600800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr20:1600200-1601000	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr20:1600200-1601200	Enhancers	Fetal Thymus	thymus
24	chr20:1600200-1601200	Flanking Active TSS	GM12878-XiMat	blood
25	chr20:1600200-1601400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr20:1600200-1601600	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr20:1600200-1602000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr20:1600200-1603400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr20:1600200-1605800	Enhancers	Primary B cells from peripheral blood	blood
30	chr20:1600400-1600600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr20:1600400-1600600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr20:1600400-1601000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr20:1600400-1601200	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr20:1600400-1601200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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