Variant report

Variant	rs11591079
Chromosome Location	chr1:159796302-159796303
allele	G/T
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	MTA3	chr1:159796118-159796820	GM12878	blood:	n/a	n/a
2	MXI1	chr1:159796277-159796590	GM12878	blood:	n/a	n/a
3	NFIC	chr1:159796214-159796640	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:159796146-159796654	HL-60	blood:	n/a	n/a
5	RCOR1	chr1:159796251-159796541	GM12878	blood:	n/a	n/a
6	BHLHE40	chr1:159796258-159796740	GM12878	blood:	n/a	n/a
7	EP300	chr1:159796250-159796585	GM12878	blood:	n/a	n/a
8	RELA	chr1:159796235-159796712	GM18505	blood:	n/a	chr1:159796587-159796596 chr1:159796587-159796596
9	MYC	chr1:159796224-159796789	NB4	blood:	n/a	chr1:159796432-159796439 chr1:159796430-159796439 chr1:159796445-159796455
10	RUNX3	chr1:159795920-159796764	GM12878	blood:	n/a	n/a
11	RUNX3	chr1:159796184-159796596	GM12878	blood:	n/a	n/a
12	EP300	chr1:159796207-159796655	GM12878	blood:	n/a	n/a
13	IKZF1	chr1:159796259-159796710	GM12878	blood:	n/a	n/a
14	ETS1	chr1:159796275-159796598	GM12878	blood:	n/a	chr1:159796545-159796560 chr1:159796400-159796411 chr1:159796399-159796413
15	MAX	chr1:159796224-159796620	K562	blood:	n/a	chr1:159796432-159796439 chr1:159796430-159796439 chr1:159796445-159796455
16	MAX	chr1:159796037-159796753	NB4	blood:	n/a	chr1:159796432-159796439 chr1:159796430-159796439 chr1:159796445-159796455
17	MAX	chr1:159796195-159796619	GM12878	blood:	n/a	chr1:159796432-159796439 chr1:159796430-159796439 chr1:159796445-159796455
18	RELA	chr1:159796255-159796742	GM12891	blood:	n/a	chr1:159796587-159796596 chr1:159796587-159796596
19	MAX	chr1:159796244-159796718	GM12878	blood:	n/a	chr1:159796432-159796439 chr1:159796430-159796439 chr1:159796445-159796455

Variant related genes	Relation type
SLAMF8	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1320570	1.00[CHB][hapmap]
rs17427209	1.00[CHB][hapmap]
rs17467492	1.00[CHB][hapmap]
rs2494495	0.88[CEU][hapmap]
rs2501343	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs2789415	1.00[CHB][hapmap]
rs2789416	1.00[CHB][hapmap]
rs2789417	1.00[CHB][hapmap]
rs2789418	1.00[CHB][hapmap]
rs2820579	1.00[CHB][hapmap]
rs2820584	1.00[CHB][hapmap]
rs2840583	1.00[CHB][hapmap]
rs2840588	1.00[CHB][hapmap]
rs3001288	1.00[CHB][hapmap]
rs4656246	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55739401	0.81[EUR][1000 genomes]
rs55742616	0.87[EUR][1000 genomes]
rs60205880	0.81[EUR][1000 genomes]
rs61821627	0.81[EUR][1000 genomes]
rs61821659	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61823160	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61823162	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61823163	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61823164	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61823165	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6427496	1.00[CEU][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6662675	1.00[CHB][hapmap]
rs6662918	1.00[CHB][hapmap]
rs72700615	0.83[EUR][1000 genomes]
rs72700621	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72700626	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72700627	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72700628	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72700632	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72700634	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7519854	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs7525794	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7527418	0.82[EUR][1000 genomes]
rs7528163	0.81[EUR][1000 genomes]
rs7549918	0.81[EUR][1000 genomes]
rs876538	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005195	chr1:159452759-159910337	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11591079	OLFML2B	cis	cerebellum	SCAN
rs11591079	OR6N2	cis	cerebellum	SCAN
rs11591079	COPA	cis	cerebellum	SCAN
rs11591079	HAPLN2	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159791000-159796600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:159792400-159796600	Enhancers	Placenta	Placenta
3	chr1:159793000-159799000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr1:159793400-159799800	Weak transcription	Lung	lung
5	chr1:159793600-159797000	Weak transcription	Gastric	stomach
6	chr1:159793800-159796800	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr1:159793800-159798800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:159794000-159807400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:159794200-159804600	Weak transcription	Fetal Intestine Small	intestine
10	chr1:159794600-159797200	Enhancers	Placenta Amnion	Placenta Amnion
11	chr1:159794600-159801000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr1:159794800-159796600	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr1:159794800-159796800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:159794800-159797200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:159794800-159798200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr1:159794800-159798600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:159794800-159798800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:159795000-159798400	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr1:159795000-159799200	Enhancers	Primary T cells from cord blood	blood
20	chr1:159795200-159796800	Enhancers	Fetal Thymus	thymus
21	chr1:159795200-159797200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:159795200-159797400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:159795200-159797400	Enhancers	Small Intestine	intestine
24	chr1:159795200-159797400	Enhancers	Thymus	Thymus
25	chr1:159795200-159798200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr1:159795200-159800200	Enhancers	Spleen	Spleen
27	chr1:159795400-159796400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr1:159795400-159796600	Weak transcription	HSMMtube	muscle
29	chr1:159795400-159797400	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr1:159795400-159797600	Enhancers	Primary hematopoietic stem cells	blood
31	chr1:159795400-159798400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:159795400-159807200	Weak transcription	Brain Substantia Nigra	brain
33	chr1:159795600-159796800	Enhancers	Dnd41	blood
34	chr1:159795600-159797600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:159795600-159798400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:159795600-159799000	Enhancers	Primary B cells from cord blood	blood
37	chr1:159795600-159799200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr1:159795800-159796400	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr1:159795800-159797000	Enhancers	Adipose Nuclei	Adipose
40	chr1:159795800-159798200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr1:159796000-159796400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:159796000-159796400	Enhancers	Colonic Mucosa	Colon
43	chr1:159796000-159796400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
44	chr1:159796000-159796600	Flanking Active TSS	GM12878-XiMat	blood
45	chr1:159796000-159796800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr1:159796000-159797200	Enhancers	Fetal Muscle Leg	muscle
47	chr1:159796000-159797200	Enhancers	Right Atrium	heart
48	chr1:159796000-159797400	Enhancers	Esophagus	oesophagus
49	chr1:159796000-159799600	Enhancers	Primary B cells from peripheral blood	blood
50	chr1:159796200-159796400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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