Variant report

Variant	rs6043506
Chromosome Location	chr20:1626843-1626844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SIRPA-3	chr20:1626682-1629118	ENSG00000237914
2	lnc-SIRPA-3	chr20:1626682-1629119	NR_110090

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10211741	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10211807	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs11698603	0.88[JPT][hapmap]
rs12625431	0.91[JPT][hapmap]
rs12625449	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1438106	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs1550266	0.91[JPT][hapmap]
rs202551	0.81[JPT][hapmap]
rs202552	0.91[JPT][hapmap]
rs2318047	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs2873613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3746719	0.87[JPT][hapmap]
rs3746720	0.87[JPT][hapmap]
rs3746721	0.87[JPT][hapmap]
rs3761271	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4254564	0.91[JPT][hapmap]
rs4254565	0.91[JPT][hapmap]
rs4254566	0.91[JPT][hapmap]
rs4353709	0.91[JPT][hapmap]
rs4473456	0.91[JPT][hapmap]
rs6034239	0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap]
rs6034307	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6034368	0.91[JPT][hapmap]
rs6034370	0.91[JPT][hapmap]
rs6043403	0.91[JPT][hapmap]
rs6043722	0.91[JPT][hapmap]
rs6043726	0.91[JPT][hapmap]
rs6110760	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7263011	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap]
rs963168	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
10	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
11	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
12	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
13	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
14	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
15	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6043506	SRXN1	cis	cerebellum	SCAN
rs6043506	SIRPD	cis	cerebellum	SCAN
rs6043506	FAM110A	cis	parietal	SCAN
rs6043506	SNORD57	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1605200-1631800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr20:1607600-1627600	Weak transcription	Fetal Thymus	thymus
3	chr20:1607600-1632000	Weak transcription	Spleen	Spleen
4	chr20:1623800-1627600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr20:1624000-1627600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr20:1624000-1629000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
7	chr20:1624400-1627000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr20:1624400-1627600	Genic enhancers	Primary T cells fromperipheralblood	blood
9	chr20:1625200-1630400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
10	chr20:1625400-1627000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr20:1625400-1632200	Weak transcription	Thymus	Thymus
12	chr20:1625600-1627800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr20:1625600-1630000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr20:1625800-1629200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr20:1626600-1627000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr20:1626600-1627600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr20:1626600-1628000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr20:1626600-1628200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr20:1626600-1631600	Genic enhancers	Primary T cells from cord blood	blood

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