Variant report

Variant	rs963168
Chromosome Location	chr20:1638578-1638579
allele	A/G
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	IKZF1	chr20:1638383-1639084	GM12878	blood:	n/a	n/a
2	POLR2A	chr20:1638102-1638640	GM12891	blood:	n/a	n/a
3	SPI1	chr20:1638068-1638826	GM12878	blood:	n/a	chr20:1638460-1638469 chr20:1638458-1638471 chr20:1638461-1638468
4	POLR2A	chr20:1638183-1638782	NB4	blood:	n/a	n/a
5	SPI1	chr20:1638303-1638609	GM12878	blood:	n/a	chr20:1638460-1638469 chr20:1638458-1638471 chr20:1638461-1638468
6	MAX	chr20:1638236-1638861	NB4	blood:	n/a	n/a
7	SPI1	chr20:1638212-1638741	HL-60	blood:	n/a	chr20:1638460-1638469 chr20:1638458-1638471 chr20:1638461-1638468
8	RUNX3	chr20:1638208-1639085	GM12878	blood:	n/a	n/a
9	SPI1	chr20:1638272-1638715	HL-60	blood:	n/a	chr20:1638460-1638469 chr20:1638458-1638471 chr20:1638461-1638468
10	POLR2A	chr20:1638122-1638666	GM12891	blood:	n/a	n/a
11	SPI1	chr20:1638317-1638649	GM12891	blood:	n/a	chr20:1638460-1638469 chr20:1638458-1638471 chr20:1638461-1638468
12	FOXM1	chr20:1638513-1639091	GM12878	blood:	n/a	n/a
13	SPI1	chr20:1638229-1638663	GM12891	blood:	n/a	chr20:1638460-1638469 chr20:1638458-1638471 chr20:1638461-1638468
14	NFIC	chr20:1638450-1639068	GM12878	blood:	n/a	n/a
15	MTA3	chr20:1638387-1638867	GM12878	blood:	n/a	n/a
16	MYC	chr20:1638207-1638853	NB4	blood:	n/a	n/a
17	PML	chr20:1638159-1638812	GM12878	blood:	n/a	n/a
18	RUNX3	chr20:1638526-1638974	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
SIRPG	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10211741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10211807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11698603	0.88[JPT][hapmap]
rs12625431	0.91[JPT][hapmap]
rs12625449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1438106	0.81[CHD][hapmap];0.91[JPT][hapmap]
rs1550266	0.91[JPT][hapmap]
rs202551	0.81[JPT][hapmap]
rs202552	0.91[JPT][hapmap]
rs2277760	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2318045	0.99[ASN][1000 genomes]
rs2318047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2873613	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3746719	0.87[JPT][hapmap]
rs3746720	0.87[JPT][hapmap]
rs3746721	0.87[JPT][hapmap]
rs3761271	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
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];0.85[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs6034307	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6034368	0.91[JPT][hapmap]
rs6034370	0.91[JPT][hapmap]
rs6043403	0.91[JPT][hapmap]
rs6043450	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6043506	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]
rs6043722	0.91[JPT][hapmap]
rs6043726	0.91[JPT][hapmap]
rs60736823	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6074957	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6105456	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6105462	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6105490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6110760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6110764	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6110773	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6110777	0.88[ASN][1000 genomes]
rs6110786	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6110828	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6110845	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6110853	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72484089	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72484092	0.80[ASN][1000 genomes]
rs7263011	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73604189	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs743080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968860	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

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
rs963168	SNORD57	cis	cerebellum	SCAN
rs963168	SIRPD	cis	cerebellum	SCAN
rs963168	SRXN1	cis	cerebellum	SCAN
rs963168	FAM110A	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1630400-1639200	Enhancers	Dnd41	blood
2	chr20:1632200-1644600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr20:1632400-1638600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr20:1632400-1642200	Weak transcription	Spleen	Spleen
5	chr20:1635000-1638800	Active TSS	Thymus	Thymus
6	chr20:1635200-1638600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr20:1636600-1638800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
8	chr20:1636600-1639000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr20:1636800-1639000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
10	chr20:1636800-1639200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr20:1637200-1639000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
12	chr20:1637400-1640600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr20:1637600-1639800	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr20:1637800-1638800	Enhancers	HMEC	breast
15	chr20:1637800-1639000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr20:1638000-1638600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr20:1638000-1638600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr20:1638000-1639000	Flanking Active TSS	Fetal Thymus	thymus
19	chr20:1638000-1639200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr20:1638200-1638600	Enhancers	Hela-S3	cervix
21	chr20:1638200-1638600	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr20:1638200-1638800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr20:1638200-1639000	Enhancers	Primary hematopoietic stem cells	blood
24	chr20:1638200-1639000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr20:1638200-1639200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr20:1638200-1639200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr20:1638200-1639200	Enhancers	GM12878-XiMat	blood
28	chr20:1638400-1638600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr20:1638400-1638800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr20:1638400-1639000	Enhancers	Primary B cells from peripheral blood	blood
31	chr20:1638400-1639400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr20:1638400-1639600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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