Variant report

Variant	rs1938595
Chromosome Location	chr11:58980812-58980813
allele	A/C
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	POU2F2	chr11:58980101-58981140	GM12891	blood:	n/a	chr11:58981069-58981076 chr11:58981066-58981080 chr11:58981068-58981077 chr11:58981068-58981079
3	TBL1XR1	chr11:58980413-58981263	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:58980201-58981137	GM12891	blood:	n/a	n/a
5	POLR2A	chr11:58977760-58981164	GM12891	blood:	n/a	n/a
6	POU2F2	chr11:58980123-58981205	GM12891	blood:	n/a	chr11:58981069-58981076 chr11:58981066-58981080 chr11:58981068-58981077 chr11:58981068-58981079
7	IKZF1	chr11:58980495-58981131	GM12878	blood:	n/a	n/a
8	PML	chr11:58979974-58981231	GM12878	blood:	n/a	n/a
9	EBF1	chr11:58980443-58981156	GM12878	blood:	n/a	chr11:58980760-58980771 chr11:58980759-58980772
10	RCOR1	chr11:58979999-58980855	GM12878	blood:	n/a	n/a
11	MAZ	chr11:58980383-58981056	GM12878	blood:	n/a	n/a
12	POLR2A	chr11:58974003-58981138	GM12891	blood:	n/a	n/a
13	EP300	chr11:58980337-58981070	GM12878	blood:	n/a	chr11:58980777-58980791
14	STAT5A	chr11:58980443-58981136	GM12878	blood:	n/a	n/a
15	BCL11A	chr11:58980517-58980930	GM12878	blood:	n/a	n/a
16	ATF2	chr11:58980128-58981382	GM12878	blood:	n/a	n/a
17	POU2F2	chr11:58980798-58981219	GM12878	blood:	n/a	chr11:58981069-58981076 chr11:58981066-58981080 chr11:58981068-58981077 chr11:58981068-58981079
18	RUNX3	chr11:58980222-58981282	GM12878	blood:	n/a	n/a
19	WRNIP1	chr11:58979782-58981064	GM12878	blood:	n/a	n/a
20	NFIC	chr11:58980210-58981293	GM12878	blood:	n/a	n/a
21	NFIC	chr11:58980154-58981331	GM12878	blood:	n/a	n/a
22	RUNX3	chr11:58980174-58981330	GM12878	blood:	n/a	n/a
23	TBP	chr11:58980262-58981258	GM12878	blood:	n/a	n/a
24	SPI1	chr11:58980008-58981024	GM12878	blood:	n/a	chr11:58980461-58980474 chr11:58980462-58980475 chr11:58980463-58980472
25	MTA3	chr11:58980322-58981124	GM12878	blood:	n/a	n/a
26	EP300	chr11:58980337-58981222	GM12878	blood:	n/a	chr11:58980777-58980791
27	POLR2A	chr11:58974021-58981115	GM12878	blood:	n/a	n/a
28	NFATC1	chr11:58980028-58981258	GM12878	blood:	n/a	chr11:58980915-58980929
29	CHD2	chr11:58980197-58981124	GM12878	blood:	n/a	n/a
30	SPI1	chr11:58980246-58981086	HL-60	blood:	n/a	chr11:58980461-58980474 chr11:58980462-58980475 chr11:58980463-58980472
31	POLR2A	chr11:58974014-58981138	GM12878	blood:	n/a	n/a
32	EBF1	chr11:58980355-58981200	GM12878	blood:	n/a	chr11:58980760-58980771 chr11:58980759-58980772
33	RELA	chr11:58980092-58981223	GM12891	blood:	n/a	n/a
34	CHD1	chr11:58980162-58980949	GM12878	blood:	n/a	n/a
35	FOXM1	chr11:58980139-58981279	GM12878	blood:	n/a	n/a
36	BCL11A	chr11:58980660-58980974	GM12878	blood:	n/a	n/a
37	CUX1	chr11:58980316-58981166	GM12878	blood:	n/a	n/a
38	POLR2A	chr11:58977264-58981276	GM19099	blood:	n/a	n/a
39	POU2F2	chr11:58980092-58981242	GM12878	blood:	n/a	chr11:58981069-58981076 chr11:58981066-58981080 chr11:58981068-58981077 chr11:58981068-58981079
40	FOXM1	chr11:58980225-58981034	GM12878	blood:	n/a	n/a
41	ATF2	chr11:58980270-58981258	GM12878	blood:	n/a	n/a
42	NFATC1	chr11:58980246-58980990	GM12878	blood:	n/a	chr11:58980915-58980929
43	BATF	chr11:58980509-58981044	GM12878	blood:	n/a	n/a
44	POLR2A	chr11:58977864-58981086	GM19193	blood:	n/a	n/a
45	BCLAF1	chr11:58980303-58981308	GM12878	blood:	n/a	chr11:58981058-58981067
46	BHLHE40	chr11:58980273-58981260	GM12878	blood:	n/a	n/a
47	POLR2A	chr11:58973489-58981285	GM12891	blood:	n/a	n/a
48	MTA3	chr11:58979755-58981287	GM12878	blood:	n/a	n/a
49	RELA	chr11:58980331-58981212	GM19099	blood:	n/a	n/a
50	POLR2A	chr11:58980105-58981034	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58937186..58939247-chr11:58980596..58982199,2	K562	blood:

Variant related genes	Relation type
MPEG1	TF binding region
ENSG00000110042	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1048696	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10501375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10501376	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10896957	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11229868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11229870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11229872	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11229873	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11229874	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11229875	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11229882	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11229889	0.88[CEU][hapmap];0.96[TSI][hapmap]
rs11229901	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11229902	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11229903	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11229904	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12223401	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]
rs12575770	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12576150	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12576412	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12576558	0.87[EUR][1000 genomes]
rs12576879	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12577252	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17153538	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35654554	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3740946	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3781796	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59466005	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60265864	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61086875	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7104296	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7104437	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7926933	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7942203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs869155	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1938595	WDR74	cis	parietal	SCAN
rs1938595	MPEG1	cis	lymphoblastoid	seeQTL
rs1938595	MPEG1	Cis_1M	lymphoblastoid	RTeQTL
rs1938595	DTX4	Cis_1M	lymphoblastoid	RTeQTL
rs1938595	CCDC86	cis	parietal	SCAN

Chromatin state (count:33 , 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	chr11:58975800-58981800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:58976000-58989400	Weak transcription	Stomach Mucosa	stomach
7	chr11:58976400-58981000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr11:58977000-58981000	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr11:58977200-58981200	Active TSS	Rectal Smooth Muscle	rectum
10	chr11:58977400-58981000	Weak transcription	HSMMtube	muscle
11	chr11:58977400-58981400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:58977600-58981600	Flanking Active TSS	GM12878-XiMat	blood
13	chr11:58977600-58984000	Weak transcription	Fetal Lung	lung
14	chr11:58978200-58981000	Flanking Active TSS	Primary B cells from peripheral blood	blood
15	chr11:58978600-58984000	Weak transcription	Colon Smooth Muscle	Colon
16	chr11:58979200-58989600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr11:58979400-58983800	Weak transcription	Fetal Stomach	stomach
18	chr11:58979800-58985200	Weak transcription	Pancreas	Pancrea
19	chr11:58980000-58981000	Enhancers	Primary hematopoietic stem cells	blood
20	chr11:58980000-58981000	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr11:58980000-58984200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr11:58980400-58981000	Enhancers	Placenta	Placenta
23	chr11:58980400-58981000	Enhancers	Spleen	Spleen
24	chr11:58980400-58982000	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr11:58980400-58984200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:58980400-58984200	Weak transcription	Fetal Thymus	thymus
27	chr11:58980400-58984400	Weak transcription	Fetal Intestine Small	intestine
28	chr11:58980400-58991200	Weak transcription	Fetal Muscle Leg	muscle
29	chr11:58980600-58981000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
30	chr11:58980600-58981200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr11:58980600-58982600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr11:58980800-58981200	Enhancers	Adipose Nuclei	Adipose
33	chr11:58980800-58983200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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