Variant report

Variant	rs3758921
Chromosome Location	chr11:57283046-57283047
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	POLR2A	chr11:57281090-57283641	HL-60	blood:	n/a	n/a
2	TBP	chr11:57281817-57283531	K562	blood:	n/a	n/a
3	UBTF	chr11:57281466-57283773	K562	blood:	n/a	n/a
4	TCF7L2	chr11:57282755-57283524	HCT-116	colon:	n/a	n/a
5	MAX	chr11:57283041-57283738	SK-N-SH	brain:	n/a	chr11:57283229-57283239
6	TAF1	chr11:57283007-57283335	PFSK-1	brain:	n/a	n/a
7	MXI1	chr11:57282580-57283673	K562	blood:	n/a	n/a
8	SPI1	chr11:57282139-57283051	HL-60	blood:	n/a	chr11:57282681-57282688
9	UBTF	chr11:57281627-57283578	K562	blood:	n/a	n/a
10	ZBTB7A	chr11:57281914-57283531	K562	blood:	n/a	chr11:57282888-57282897 chr11:57283394-57283403
11	EGR1	chr11:57282092-57283425	K562	blood:	n/a	chr11:57282900-57282911 chr11:57282900-57282910 chr11:57283231-57283241 chr11:57282899-57282912 chr11:57283017-57283026 chr11:57282899-57282912 chr11:57282900-57282909 chr11:57282681-57282690 chr11:57282888-57282901 chr11:57282900-57282911 chr11:57283232-57283245 chr11:57283229-57283239 chr11:57282889-57282899 chr11:57282896-57282910 chr11:57283226-57283239 chr11:57282899-57282912 chr11:57282900-57282910 chr11:57282899-57282912 chr11:57282898-57282912
12	POLR2A	chr11:57282697-57283080	H1-neurons	neurons:	n/a	n/a
13	MAX	chr11:57282917-57283589	K562	blood:	n/a	chr11:57283229-57283239
14	FOXA2	chr11:57282855-57283537	A549	lung:	n/a	n/a
15	FOXP2	chr11:57282922-57283390	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr11:57282039-57283575	K562	blood:	n/a	n/a
17	POLR2A	chr11:57281720-57283555	GM12878	blood:	n/a	n/a
18	EGR1	chr11:57282214-57283383	K562	blood:	n/a	chr11:57282900-57282911 chr11:57282900-57282910 chr11:57283231-57283241 chr11:57282899-57282912 chr11:57283017-57283026 chr11:57282899-57282912 chr11:57282900-57282909 chr11:57282681-57282690 chr11:57282888-57282901 chr11:57282900-57282911 chr11:57283232-57283245 chr11:57283229-57283239 chr11:57282889-57282899 chr11:57282896-57282910 chr11:57283226-57283239 chr11:57282899-57282912 chr11:57282900-57282910 chr11:57282899-57282912 chr11:57282898-57282912
19	POLR2A	chr11:57281645-57283571	K562	blood:	n/a	n/a
20	CTCF	chr11:57282900-57283050	GM12874	blood:	n/a	n/a
21	TCF12	chr11:57282921-57283439	A549	lung:	n/a	n/a
22	POLR2A	chr11:57281888-57283712	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr11:57281402-57283699	K562	blood:	n/a	n/a
24	POLR2A	chr11:57282841-57283392	HepG2	liver:	n/a	n/a
25	USF1	chr11:57283015-57283535	H1-hESC	embryonic stem cell:	n/a	chr11:57283281-57283290 chr11:57283279-57283290 chr11:57283280-57283289 chr11:57283280-57283289
26	JUND	chr11:57282059-57283437	K562	blood:	n/a	chr11:57282388-57282397
27	POLR2A	chr11:57282874-57283608	HepG2	liver:	n/a	n/a
28	POLR2A	chr11:57281594-57283512	GM18951	blood:	n/a	n/a
29	HMGN3	chr11:57281508-57283551	K562	blood:	n/a	n/a
30	SIN3AK20	chr11:57282813-57283392	K562	blood:	n/a	n/a
31	BHLHE40	chr11:57281148-57283762	K562	blood:	n/a	chr11:57282437-57282453 chr11:57283281-57283290 chr11:57283280-57283289 chr11:57282445-57282461 chr11:57283280-57283289 chr11:57282434-57282450 chr11:57282427-57282443
32	JUN	chr11:57282909-57283175	H1-hESC	embryonic stem cell:	n/a	n/a
33	TAF1	chr11:57281700-57283402	HepG2	liver:	n/a	n/a
34	POLR2A	chr11:57283039-57283415	MCF-7	breast:	n/a	n/a
35	POLR2A	chr11:57283041-57283439	MCF-7	breast:	n/a	n/a
36	POLR2A	chr11:57281596-57283522	GM18505	blood:	n/a	n/a
37	POLR2A	chr11:57282809-57283364	GM12892	blood:	n/a	n/a
38	CBX3	chr11:57282793-57283406	K562	blood:	n/a	n/a
39	POLR2A	chr11:57282710-57283658	HUVEC	blood vessel:	n/a	n/a
40	CTCF	chr11:57282980-57283130	GM12865	blood:	n/a	n/a
41	MAX	chr11:57282934-57283529	H1-hESC	embryonic stem cell:	n/a	chr11:57283229-57283239
42	MAX	chr11:57282795-57283671	A549	lung:	n/a	chr11:57283229-57283239
43	CTBP2	chr11:57281662-57283440	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr11:57282969-57283565	HCT-116	colon:	n/a	n/a
45	MAX	chr11:57282773-57283636	SK-N-SH	brain:	n/a	chr11:57283229-57283239
46	ZBTB7A	chr11:57282653-57283644	ECC-1	luminal epithelium:	n/a	chr11:57282888-57282897 chr11:57283394-57283403
47	SIN3A	chr11:57281214-57283753	H1-hESC	embryonic stem cell:	n/a	chr11:57281841-57281852 chr11:57281954-57281965
48	POLR2A	chr11:57282653-57283375	GM12878	blood:	n/a	n/a
49	MYC	chr11:57281401-57283820	K562	blood:	n/a	chr11:57282432-57282442 chr11:57283229-57283239
50	MYBL2	chr11:57282903-57283653	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:57095142..57097690-chr11:57281751..57283331,2	K562	blood:
2	chr11:57282855..57283355-chr6:97284984..97285522,2	HCT-116	colon:
3	chr11:57279697..57283964-chr11:57296063..57300992,5	K562	blood:
4	chr11:57260838..57262632-chr11:57281221..57283072,2	K562	blood:
5	chr11:57264825..57270955-chr11:57280277..57284813,10	K562	blood:
6	chr11:57265680..57269520-chr11:57278275..57283954,6	K562	blood:
7	chr11:57102611..57104475-chr11:57280670..57283217,2	K562	blood:
8	chr11:57279377..57284601-chr11:57296598..57300992,7	K562	blood:

Variant related genes	Relation type
SLC43A1	TF binding region
ENSG00000149136	Chromatin interaction
ENSG00000238692	Chromatin interaction
ENSG00000112218	Chromatin interaction
ENSG00000134809	Chromatin interaction
ENSG00000149150	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10896623	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12277281	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3851118	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4938870	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4939148	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7109985	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7110678	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7925116	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3758921	TIMM10	cis	lung	GTEx
rs3758921	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs3758921	SMTNL1	cis	Adipose Subcutaneous	GTEx
rs3758921	TIMM10	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57280400-57283600	Active TSS	Pancreas	Pancrea
2	chr11:57280600-57284000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr11:57280600-57284000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:57280800-57283800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr11:57281000-57284000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr11:57281200-57283400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr11:57281200-57283600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr11:57281200-57283800	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr11:57281200-57284000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr11:57281200-57284000	Active TSS	GM12878-XiMat	blood
11	chr11:57281400-57283200	Active TSS	Brain Cingulate Gyrus	brain
12	chr11:57281400-57283400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr11:57281400-57283400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr11:57281400-57283400	Active TSS	Ovary	ovary
15	chr11:57281400-57283400	Active TSS	Rectal Smooth Muscle	rectum
16	chr11:57281400-57283600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr11:57281400-57283600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr11:57281400-57283600	Active TSS	Primary T cells from cord blood	blood
19	chr11:57281400-57283600	Active TSS	Left Ventricle	heart
20	chr11:57281400-57283600	Active TSS	NHLF	lung
21	chr11:57281400-57283800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
22	chr11:57281400-57283800	Active TSS	Right Ventricle	heart
23	chr11:57281400-57284000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:57281600-57283200	Active TSS	Brain Substantia Nigra	brain
25	chr11:57281600-57283400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:57281600-57283400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr11:57281600-57283400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:57281600-57283400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr11:57281600-57283400	Bivalent Enhancer	Fetal Brain Male	brain
30	chr11:57281600-57283400	Active TSS	Psoas Muscle	Psoas
31	chr11:57281600-57283600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:57281600-57283600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr11:57281600-57283600	Active TSS	Muscle Satellite Cultured Cells	--
34	chr11:57281600-57283600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
35	chr11:57281600-57283600	Flanking Active TSS	Colonic Mucosa	Colon
36	chr11:57281600-57283600	Active TSS	Colon Smooth Muscle	Colon
37	chr11:57281600-57283800	Active TSS	Brain Anterior Caudate	brain
38	chr11:57281600-57283800	Active TSS	Right Atrium	heart
39	chr11:57281600-57283800	Active TSS	HSMM	muscle
40	chr11:57281600-57284000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr11:57281600-57284000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
42	chr11:57281800-57283200	Active TSS	Gastric	stomach
43	chr11:57281800-57283400	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr11:57281800-57283400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr11:57281800-57283400	Active TSS	Liver	Liver
46	chr11:57281800-57283400	Active TSS	Small Intestine	intestine
47	chr11:57281800-57283600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr11:57281800-57283600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr11:57281800-57283600	Active TSS	Aorta	Aorta
50	chr11:57281800-57283600	Active TSS	Brain Angular Gyrus	brain

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