Variant report

Variant	rs6591509
Chromosome Location	chr11:58980549-58980550
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	POLR2A	chr11:58977761-58981077	GM12891	blood:	n/a	n/a
2	SPI1	chr11:58980247-58980637	GM12878	blood:	n/a	chr11:58980461-58980474 chr11:58980462-58980475 chr11:58980463-58980472
3	POU2F2	chr11:58980101-58981140	GM12891	blood:	n/a	chr11:58981069-58981076 chr11:58981066-58981080 chr11:58981068-58981077 chr11:58981068-58981079
4	TBL1XR1	chr11:58980413-58981263	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:58980201-58981137	GM12891	blood:	n/a	n/a
6	POLR2A	chr11:58977760-58981164	GM12891	blood:	n/a	n/a
7	POU2F2	chr11:58980123-58981205	GM12891	blood:	n/a	chr11:58981069-58981076 chr11:58981066-58981080 chr11:58981068-58981077 chr11:58981068-58981079
8	IKZF1	chr11:58980495-58981131	GM12878	blood:	n/a	n/a
9	SPI1	chr11:58980269-58980641	GM12891	blood:	n/a	chr11:58980461-58980474 chr11:58980462-58980475 chr11:58980463-58980472
10	PML	chr11:58979974-58981231	GM12878	blood:	n/a	n/a
11	EBF1	chr11:58980443-58981156	GM12878	blood:	n/a	chr11:58980760-58980771 chr11:58980759-58980772
12	RCOR1	chr11:58979999-58980855	GM12878	blood:	n/a	n/a
13	MAZ	chr11:58980383-58981056	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:58974003-58981138	GM12891	blood:	n/a	n/a
15	EP300	chr11:58980337-58981070	GM12878	blood:	n/a	chr11:58980777-58980791
16	STAT5A	chr11:58980443-58981136	GM12878	blood:	n/a	n/a
17	STAT1	chr11:58980378-58980605	GM12878	blood:	n/a	n/a
18	BCL11A	chr11:58980517-58980930	GM12878	blood:	n/a	n/a
19	ATF2	chr11:58980128-58981382	GM12878	blood:	n/a	n/a
20	RUNX3	chr11:58980222-58981282	GM12878	blood:	n/a	n/a
21	SPI1	chr11:58980218-58980732	GM12891	blood:	n/a	chr11:58980461-58980474 chr11:58980462-58980475 chr11:58980463-58980472
22	WRNIP1	chr11:58979782-58981064	GM12878	blood:	n/a	n/a
23	NFIC	chr11:58980210-58981293	GM12878	blood:	n/a	n/a
24	NFIC	chr11:58980154-58981331	GM12878	blood:	n/a	n/a
25	RUNX3	chr11:58980174-58981330	GM12878	blood:	n/a	n/a
26	TBP	chr11:58980262-58981258	GM12878	blood:	n/a	n/a
27	SPI1	chr11:58980008-58981024	GM12878	blood:	n/a	chr11:58980461-58980474 chr11:58980462-58980475 chr11:58980463-58980472
28	MTA3	chr11:58980322-58981124	GM12878	blood:	n/a	n/a
29	EP300	chr11:58980337-58981222	GM12878	blood:	n/a	chr11:58980777-58980791
30	POLR2A	chr11:58974021-58981115	GM12878	blood:	n/a	n/a
31	NFATC1	chr11:58980028-58981258	GM12878	blood:	n/a	chr11:58980915-58980929
32	CHD2	chr11:58980197-58981124	GM12878	blood:	n/a	n/a
33	PML	chr11:58980313-58980630	GM12878	blood:	n/a	n/a
34	SPI1	chr11:58980246-58981086	HL-60	blood:	n/a	chr11:58980461-58980474 chr11:58980462-58980475 chr11:58980463-58980472
35	POLR2A	chr11:58974014-58981138	GM12878	blood:	n/a	n/a
36	EBF1	chr11:58980355-58981200	GM12878	blood:	n/a	chr11:58980760-58980771 chr11:58980759-58980772
37	RELA	chr11:58980092-58981223	GM12891	blood:	n/a	n/a
38	CHD1	chr11:58980162-58980949	GM12878	blood:	n/a	n/a
39	FOXM1	chr11:58980139-58981279	GM12878	blood:	n/a	n/a
40	CUX1	chr11:58980316-58981166	GM12878	blood:	n/a	n/a
41	POLR2A	chr11:58977264-58981276	GM19099	blood:	n/a	n/a
42	POU2F2	chr11:58980092-58981242	GM12878	blood:	n/a	chr11:58981069-58981076 chr11:58981066-58981080 chr11:58981068-58981077 chr11:58981068-58981079
43	FOXM1	chr11:58980225-58981034	GM12878	blood:	n/a	n/a
44	ATF2	chr11:58980270-58981258	GM12878	blood:	n/a	n/a
45	NFATC1	chr11:58980246-58980990	GM12878	blood:	n/a	chr11:58980915-58980929
46	BATF	chr11:58980509-58981044	GM12878	blood:	n/a	n/a
47	SPI1	chr11:58980374-58980579	GM12878	blood:	n/a	chr11:58980461-58980474 chr11:58980462-58980475 chr11:58980463-58980472
48	SPI1	chr11:58980292-58980712	HL-60	blood:	n/a	chr11:58980461-58980474 chr11:58980462-58980475 chr11:58980463-58980472
49	POLR2A	chr11:58977864-58981086	GM19193	blood:	n/a	n/a
50	BCLAF1	chr11:58980303-58981308	GM12878	blood:	n/a	chr11:58981058-58981067

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:58980502-58980552	Hepatocyte	liver:	n/a
2	chr11:58980502-58980552	NT2-D1	testis:	n/a
3	chr11:58980502-58980552	HUVEC	blood vessel:	n/a
4	chr11:58980502-58980552	GM12892	blood:	n/a
5	chr11:58980502-58980552	GM12878	blood:	n/a
6	chr11:58980502-58980552	HCM	heart:	n/a
7	chr11:58980502-58980552	HPAEpiC	pulmonary alveolar:	n/a
8	chr11:58980502-58980552	AG04450	lung:	fetal
9	chr11:58980502-58980552	AG10803	skin:	n/a
10	chr11:58980502-58980552	ProgFib	skin:	n/a
11	chr11:58980502-58980552	HEEpiC	esophagus:	n/a
12	chr11:58980502-58980552	HIPEpiC	eye:	n/a
13	chr11:58980502-58980552	Hela-S3	cervix:	n/a
14	chr11:58980502-58980552	BJ	skin:	n/a
15	chr11:58980502-58980552	U87	brain:	n/a
16	chr11:58980502-58980552	T-47D	breast:	n/a
17	chr11:58980502-58980552	BE2_C	brain:	n/a
18	chr11:58980502-58980552	MCF-7	breast:	n/a
19	chr11:58980502-58980552	CMK	blood:	n/a
20	chr11:58980502-58980552	HCPEpiC	choroid plexus:	n/a
21	chr11:58980502-58980552	H1-hESC	embryonic stem cell:	embryo
22	chr11:58980502-58980552	SAEC	small airway:	n/a
23	chr11:58980502-58980552	ECC-1	luminal epithelium:	n/a
24	chr11:58980502-58980552	AG09309	skin:	n/a
25	chr11:58980502-58980552	RPTEC	kidney:	n/a
26	chr11:58980502-58980552	AG09319	gingival:	n/a
27	chr11:58980502-58980552	HEK293	kidney:	embryo
28	chr11:58980502-58980552	LNCaP	prostate:	n/a
29	chr11:58980502-58980552	AG04449	skin:	fetal
30	chr11:58980502-58980552	NHDF-neo	bronchial:	n/a
31	chr11:58980502-58980552	MCF10A-Er-Src	breast:	n/a
32	chr11:58980502-58980552	SK-N-SH	brain:	n/a
33	chr11:58980502-58980552	NHBE	bronchial:	n/a
34	chr11:58980502-58980552	HL-60	blood:	n/a
35	chr11:58980502-58980552	ovcar-3	ovarian:	n/a
36	chr11:58980502-58980552	HCF	heart:	n/a
37	chr11:58980502-58980552	PANC-1	pancreas:	n/a
38	chr11:58980502-58980552	NB4	blood:	n/a
39	chr11:58980502-58980552	IMR90	lung:	fetal
40	chr11:58980502-58980552	SKMC	muscle:	n/a
41	chr11:58980502-58980552	SK-N-SH_RA	brain:	n/a
42	chr11:58980502-58980552	GM12891	blood:	n/a
43	chr11:58980502-58980552	HRPEpiC	eye:	n/a
44	chr11:58980502-58980552	HMEC	breast:	n/a
45	chr11:58980502-58980552	GM19239	blood:	n/a
46	chr11:58980502-58980552	HRCEpiC	kidney:	n/a
47	chr11:58980502-58980552	GM06990	blood:	n/a
48	chr11:58980502-58980552	A549	lung:	n/a
49	chr11:58980502-58980552	K562	blood:	n/a
50	chr11:58980502-58980552	HAEpiC	amniotic membrane:	n/a

Variant related genes	Relation type
MPEG1	TF binding region
MPEG1	CpG island

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11600401	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11606140	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11607278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11607673	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12419479	0.88[CEU][hapmap];0.89[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2000478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2211912	0.96[CEU][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34697089	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3944255	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4369428	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4939269	0.89[CEU][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs5029315	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs610123	1.00[CEU][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61903328	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs656163	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs7113633	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7113936	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7131079	0.92[CEU][hapmap];0.89[CHB][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7928981	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7942710	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7944135	1.00[CEU][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7944319	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952377	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv3351601	chr11:58979308-59052763	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6591509	SNORD28	cis	cerebellum	SCAN
rs6591509	UBE2L6	cis	parietal	SCAN
rs6591509	OR5B2	cis	parietal	SCAN
rs6591509	DTX4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58973400-58983200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr11:58973600-58982000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:58973800-58984000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr11:58975400-58986600	Weak transcription	Gastric	stomach
5	chr11:58975800-58980800	Active TSS	Adipose Nuclei	Adipose
6	chr11:58975800-58981800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:58976000-58989400	Weak transcription	Stomach Mucosa	stomach
8	chr11:58976400-58981000	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr11:58977000-58981000	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr11:58977200-58981200	Active TSS	Rectal Smooth Muscle	rectum
11	chr11:58977400-58981000	Weak transcription	HSMMtube	muscle
12	chr11:58977400-58981400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:58977600-58981600	Flanking Active TSS	GM12878-XiMat	blood
14	chr11:58977600-58984000	Weak transcription	Fetal Lung	lung
15	chr11:58977800-58980600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
16	chr11:58978200-58981000	Flanking Active TSS	Primary B cells from peripheral blood	blood
17	chr11:58978600-58984000	Weak transcription	Colon Smooth Muscle	Colon
18	chr11:58979200-58989600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:58979400-58983800	Weak transcription	Fetal Stomach	stomach
20	chr11:58979800-58985200	Weak transcription	Pancreas	Pancrea
21	chr11:58980000-58980800	Active TSS	Brain Hippocampus Middle	brain
22	chr11:58980000-58981000	Enhancers	Primary hematopoietic stem cells	blood
23	chr11:58980000-58981000	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr11:58980000-58984200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr11:58980200-58980600	Active TSS	Monocytes-CD14+_RO01746	blood
26	chr11:58980200-58980800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:58980400-58980600	Active TSS	Primary monocytes fromperipheralblood	blood
28	chr11:58980400-58980600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr11:58980400-58981000	Enhancers	Placenta	Placenta
30	chr11:58980400-58981000	Enhancers	Spleen	Spleen
31	chr11:58980400-58982000	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr11:58980400-58984200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr11:58980400-58984200	Weak transcription	Fetal Thymus	thymus
34	chr11:58980400-58984400	Weak transcription	Fetal Intestine Small	intestine
35	chr11:58980400-58991200	Weak transcription	Fetal Muscle Leg	muscle

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