Variant report

Variant	rs1938593
Chromosome Location	chr11:58984717-58984718
allele	C/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	RELA	chr11:58984025-58984817	GM18505	blood:	n/a	n/a
2	STAT1	chr11:58984155-58984720	GM12878	blood:	n/a	chr11:58984476-58984483
3	RELA	chr11:58983980-58984877	GM19099	blood:	n/a	n/a
4	SP1	chr11:58983940-58984772	GM12878	blood:	n/a	n/a
5	RXRA	chr11:58984101-58984719	GM12878	blood:	n/a	chr11:58984449-58984458
6	ATF2	chr11:58983830-58984962	GM12878	blood:	n/a	n/a
7	POLR2A	chr11:58983973-58984862	GM12892	blood:	n/a	n/a
8	CREB1	chr11:58984006-58984885	GM12878	blood:	n/a	n/a
9	PAX5	chr11:58984033-58984737	GM12878	blood:	n/a	chr11:58984452-58984461 chr11:58984449-58984458
10	PAX5	chr11:58983901-58984896	GM12878	blood:	n/a	chr11:58984452-58984461 chr11:58984449-58984458
11	MXI1	chr11:58984032-58984770	GM12878	blood:	n/a	n/a
12	FOS	chr11:58984375-58984777	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr11:58984191-58984772	HL-60	blood:	n/a	n/a
14	RUNX3	chr11:58983838-58985112	GM12878	blood:	n/a	n/a
15	MAZ	chr11:58984140-58984766	GM12878	blood:	n/a	n/a
16	STAT3	chr11:58984041-58984820	GM12878	blood:	n/a	chr11:58984476-58984483
17	STAT5A	chr11:58983968-58985011	GM12878	blood:	n/a	chr11:58984476-58984483
18	IRF4	chr11:58983848-58984869	GM12878	blood:	n/a	n/a
19	CREB1	chr11:58983961-58984861	GM12878	blood:	n/a	n/a
20	CEBPB	chr11:58984086-58984728	GM12878	blood:	n/a	n/a
21	TCF12	chr11:58983998-58984781	GM12878	blood:	n/a	chr11:58984598-58984605
22	BATF	chr11:58984024-58984785	GM12878	blood:	n/a	n/a
23	BCLAF1	chr11:58983977-58984746	GM12878	blood:	n/a	chr11:58984449-58984458
24	POLR2A	chr11:58984092-58984764	GM12891	blood:	n/a	n/a
25	EP300	chr11:58983922-58984792	GM12878	blood:	n/a	chr11:58984473-58984482 chr11:58984144-58984158 chr11:58984449-58984463
26	PML	chr11:58983861-58985185	GM12878	blood:	n/a	n/a
27	RELA	chr11:58983983-58984936	GM19193	blood:	n/a	n/a
28	CUX1	chr11:58984052-58985053	GM12878	blood:	n/a	n/a
29	EP300	chr11:58984048-58984820	GM12878	blood:	n/a	chr11:58984473-58984482 chr11:58984144-58984158 chr11:58984449-58984463
30	SPI1	chr11:58983867-58984860	GM12891	blood:	n/a	chr11:58984226-58984239 chr11:58984228-58984237 chr11:58984449-58984458 chr11:58984225-58984238 chr11:58984610-58984623
31	RELA	chr11:58983871-58984949	GM18951	blood:	n/a	n/a
32	PAX5	chr11:58984111-58984740	GM12878	blood:	n/a	chr11:58984452-58984461 chr11:58984449-58984458
33	IRF4	chr11:58983877-58984874	GM12878	blood:	n/a	n/a
34	TBL1XR1	chr11:58983973-58984937	GM12878	blood:	n/a	n/a
35	EBF1	chr11:58984066-58984763	GM12878	blood:	n/a	n/a
36	CHD2	chr11:58984063-58984802	GM12878	blood:	n/a	n/a
37	POU2F2	chr11:58984009-58984760	GM12878	blood:	n/a	chr11:58984317-58984330 chr11:58984317-58984330 chr11:58984318-58984332 chr11:58984317-58984330
38	CEBPB	chr11:58983839-58984882	GM12878	blood:	n/a	n/a
39	RELA	chr11:58983952-58985051	GM15510	blood:	n/a	n/a
40	IKZF1	chr11:58983887-58985123	GM12878	blood:	n/a	n/a
41	FOXM1	chr11:58983923-58985000	GM12878	blood:	n/a	n/a
42	MTA3	chr11:58983890-58984879	GM12878	blood:	n/a	n/a
43	YY1	chr11:58984186-58984731	GM12891	blood:	n/a	n/a
44	BCL3	chr11:58983982-58984768	GM12878	blood:	n/a	chr11:58984449-58984458
45	BATF	chr11:58983806-58984982	GM12878	blood:	n/a	n/a
46	BCL11A	chr11:58983913-58984830	GM12878	blood:	n/a	chr11:58984449-58984458
47	EBF1	chr11:58984055-58984784	GM12878	blood:	n/a	n/a
48	TCF12	chr11:58984161-58984816	SK-N-SH	brain:	n/a	chr11:58984598-58984605
49	RAD21	chr11:58984154-58984732	GM12878	blood:	n/a	n/a
50	JUND	chr11:58984043-58984727	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
MPEG1	TF binding region
RN7SL42P	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1048444	0.96[CEU][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10792228	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10896953	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10896956	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10896958	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11229896	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11229898	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11229899	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11600294	0.85[AMR][1000 genomes]
rs12280107	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17153461	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1945592	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1945593	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2000875	0.89[ASW][hapmap];0.96[CEU][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3847	0.96[CEU][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4938915	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4939260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4939263	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4939267	0.96[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4939269	0.80[MEX][hapmap]
rs5023474	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5023475	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61689139	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6591510	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6591515	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6591517	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7109866	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7111287	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7113607	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7121247	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7129035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129362	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7931234	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7938115	0.88[AMR][1000 genomes];0.89[EUR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1938593	UBE2L6	cis	parietal	SCAN
rs1938593	CYBASC3	cis	cerebellum	SCAN
rs1938593	SNORD28	cis	cerebellum	SCAN
rs1938593	CYBASC3	cis	parietal	SCAN
rs1938593	DTX4	Cis_1M	lymphoblastoid	RTeQTL
rs1938593	MPEG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58975400-58986600	Weak transcription	Gastric	stomach
2	chr11:58976000-58989400	Weak transcription	Stomach Mucosa	stomach
3	chr11:58979200-58989600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr11:58979800-58985200	Weak transcription	Pancreas	Pancrea
5	chr11:58980400-58991200	Weak transcription	Fetal Muscle Leg	muscle
6	chr11:58981000-58991600	Weak transcription	Spleen	Spleen
7	chr11:58982800-58986000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr11:58983000-58985200	Enhancers	Primary hematopoietic stem cells	blood
9	chr11:58983200-58985000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr11:58983600-58985000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:58983600-58985000	Flanking Active TSS	GM12878-XiMat	blood
12	chr11:58983600-58985200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr11:58983800-58985000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:58983800-58985400	Enhancers	Fetal Stomach	stomach
15	chr11:58984000-58984800	Enhancers	Primary T cells from cord blood	blood
16	chr11:58984000-58984800	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr11:58984000-58984800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:58984000-58984800	Flanking Active TSS	NHDF-Ad	bronchial
19	chr11:58984000-58985000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr11:58984000-58985000	Enhancers	Colon Smooth Muscle	Colon
21	chr11:58984000-58985000	Enhancers	HMEC	breast
22	chr11:58984000-58985000	Enhancers	NHEK	skin
23	chr11:58984000-58985200	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr11:58984000-58985200	Enhancers	Fetal Kidney	kidney
25	chr11:58984000-58985200	Enhancers	Fetal Lung	lung
26	chr11:58984000-58985800	Enhancers	Adipose Nuclei	Adipose
27	chr11:58984200-58984800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr11:58984200-58984800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr11:58984200-58984800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr11:58984200-58984800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr11:58984200-58984800	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr11:58984200-58984800	Active TSS	Stomach Smooth Muscle	stomach
33	chr11:58984200-58985000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:58984200-58985000	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr11:58984200-58985000	Enhancers	Osteobl	bone
36	chr11:58984200-58985200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:58984200-58988200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr11:58984400-58984800	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr11:58984400-58984800	Enhancers	Thymus	Thymus
40	chr11:58984400-58984800	Enhancers	Hela-S3	cervix
41	chr11:58984400-58985000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr11:58984400-58985000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr11:58984400-58985000	Enhancers	Fetal Intestine Small	intestine
44	chr11:58984400-58986200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr11:58984400-58990600	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr11:58984600-58984800	Enhancers	Muscle Satellite Cultured Cells	--
47	chr11:58984600-58984800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr11:58984600-58984800	Bivalent Enhancer	HSMMtube	muscle
49	chr11:58984600-58984800	Flanking Active TSS	NHLF	lung
50	chr11:58984600-58985000	Flanking Active TSS	Primary B cells from peripheral blood	blood

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