Variant report

Variant	rs12277281
Chromosome Location	chr11:57282823-57282824
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	chr11:57281090-57283641	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	MXI1	chr11:57282580-57283673	K562	blood:	n/a	n/a
6	SPI1	chr11:57282139-57283051	HL-60	blood:	n/a	chr11:57282681-57282688
7	UBTF	chr11:57281627-57283578	K562	blood:	n/a	n/a
8	ZBTB7A	chr11:57281914-57283531	K562	blood:	n/a	chr11:57282888-57282897 chr11:57283394-57283403
9	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
10	POLR2A	chr11:57282697-57283080	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr11:57282039-57283575	K562	blood:	n/a	n/a
12	POLR2A	chr11:57281720-57283555	GM12878	blood:	n/a	n/a
13	EGR1	chr11:57282785-57283007	GM12878	blood:	n/a	chr11:57282900-57282911 chr11:57282900-57282910 chr11:57282899-57282912 chr11:57282899-57282912 chr11:57282900-57282909 chr11:57282888-57282901 chr11:57282900-57282911 chr11:57282889-57282899 chr11:57282896-57282910 chr11:57282899-57282912 chr11:57282900-57282910 chr11:57282899-57282912 chr11:57282898-57282912
14	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
15	POLR2A	chr11:57281645-57283571	K562	blood:	n/a	n/a
16	POLR2A	chr11:57281888-57283712	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr11:57281402-57283699	K562	blood:	n/a	n/a
18	JUND	chr11:57282059-57283437	K562	blood:	n/a	chr11:57282388-57282397
19	POLR2A	chr11:57281594-57283512	GM18951	blood:	n/a	n/a
20	HMGN3	chr11:57281508-57283551	K562	blood:	n/a	n/a
21	SIN3AK20	chr11:57282813-57283392	K562	blood:	n/a	n/a
22	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
23	TAF1	chr11:57281700-57283402	HepG2	liver:	n/a	n/a
24	ZNF143	chr11:57282503-57282911	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr11:57281596-57283522	GM18505	blood:	n/a	n/a
26	POLR2A	chr11:57282809-57283364	GM12892	blood:	n/a	n/a
27	CBX3	chr11:57282793-57283406	K562	blood:	n/a	n/a
28	POLR2A	chr11:57282710-57283658	HUVEC	blood vessel:	n/a	n/a
29	MAX	chr11:57282795-57283671	A549	lung:	n/a	chr11:57283229-57283239
30	CTBP2	chr11:57281662-57283440	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr11:57282820-57282970	GM12878	blood:	n/a	n/a
32	MAX	chr11:57282773-57283636	SK-N-SH	brain:	n/a	chr11:57283229-57283239
33	ZBTB7A	chr11:57282653-57283644	ECC-1	luminal epithelium:	n/a	chr11:57282888-57282897 chr11:57283394-57283403
34	SIN3A	chr11:57281214-57283753	H1-hESC	embryonic stem cell:	n/a	chr11:57281841-57281852 chr11:57281954-57281965
35	POLR2A	chr11:57282653-57283375	GM12878	blood:	n/a	n/a
36	POLR2A	chr11:57281991-57282867	K562	blood:	n/a	n/a
37	MYC	chr11:57281401-57283820	K562	blood:	n/a	chr11:57282432-57282442 chr11:57283229-57283239
38	EP300	chr11:57282489-57282825	GM12878	blood:	n/a	n/a
39	POLR2A	chr11:57281521-57283618	HL-60	blood:	n/a	n/a
40	POLR2A	chr11:57281514-57283520	GM15510	blood:	n/a	n/a
41	NR2F2	chr11:57281925-57283705	K562	blood:	n/a	n/a
42	TAF1	chr11:57282771-57283370	HepG2	liver:	n/a	n/a
43	MTA3	chr11:57281614-57283093	GM12878	blood:	n/a	n/a
44	CHD2	chr11:57282017-57283573	GM12878	blood:	n/a	chr11:57282227-57282237 chr11:57282427-57282437 chr11:57282835-57282845 chr11:57282458-57282468
45	E2F6	chr11:57282737-57283363	K562	blood:	n/a	chr11:57283015-57283024 chr11:57283231-57283240 chr11:57283017-57283026 chr11:57282887-57282896
46	CTCF	chr11:57282760-57282910	GM12865	blood:	n/a	n/a
47	YY1	chr11:57282107-57282948	HepG2	liver:	n/a	chr11:57282432-57282446 chr11:57282437-57282446 chr11:57282437-57282448 chr11:57282437-57282451
48	ETS1	chr11:57282746-57283429	K562	blood:	n/a	chr11:57283229-57283240
49	POLR2A	chr11:57281477-57283558	NB4	blood:	n/a	n/a
50	EGR1	chr11:57282683-57283009	ECC-1	luminal epithelium:	n/a	chr11:57282900-57282911 chr11:57282900-57282910 chr11:57282899-57282912 chr11:57282899-57282912 chr11:57282900-57282909 chr11:57282888-57282901 chr11:57282900-57282911 chr11:57282889-57282899 chr11:57282896-57282910 chr11:57282899-57282912 chr11:57282900-57282910 chr11:57282899-57282912 chr11:57282898-57282912

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

Variant related genes	Relation type
SLC43A1	TF binding region
ENSG00000238692	Chromatin interaction
ENSG00000149136	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	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3758921	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3851118	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4938870	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4939148	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7109985	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7110678	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7925116	0.88[AMR][1000 genomes];0.89[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
rs12277281	TIMM10	cis	Esophagus Muscularis	GTEx
rs12277281	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs12277281	TIMM10	cis	lung	GTEx
rs12277281	SMTNL1	cis	Adipose Subcutaneous	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	chr11:57281400-57283000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr11:57281400-57283200	Active TSS	Brain Cingulate Gyrus	brain
13	chr11:57281400-57283400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr11:57281400-57283400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr11:57281400-57283400	Active TSS	Ovary	ovary
16	chr11:57281400-57283400	Active TSS	Rectal Smooth Muscle	rectum
17	chr11:57281400-57283600	Active TSS	H9 Cell Line	embryonic stem cell
18	chr11:57281400-57283600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
19	chr11:57281400-57283600	Active TSS	Primary T cells from cord blood	blood
20	chr11:57281400-57283600	Active TSS	Left Ventricle	heart
21	chr11:57281400-57283600	Active TSS	NHLF	lung
22	chr11:57281400-57283800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
23	chr11:57281400-57283800	Active TSS	Right Ventricle	heart
24	chr11:57281400-57284000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:57281600-57283000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
26	chr11:57281600-57283000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr11:57281600-57283200	Active TSS	Brain Substantia Nigra	brain
28	chr11:57281600-57283400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr11:57281600-57283400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
30	chr11:57281600-57283400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr11:57281600-57283400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:57281600-57283400	Bivalent Enhancer	Fetal Brain Male	brain
33	chr11:57281600-57283400	Active TSS	Psoas Muscle	Psoas
34	chr11:57281600-57283600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr11:57281600-57283600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr11:57281600-57283600	Active TSS	Muscle Satellite Cultured Cells	--
37	chr11:57281600-57283600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
38	chr11:57281600-57283600	Flanking Active TSS	Colonic Mucosa	Colon
39	chr11:57281600-57283600	Active TSS	Colon Smooth Muscle	Colon
40	chr11:57281600-57283800	Active TSS	Brain Anterior Caudate	brain
41	chr11:57281600-57283800	Active TSS	Right Atrium	heart
42	chr11:57281600-57283800	Active TSS	HSMM	muscle
43	chr11:57281600-57284000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr11:57281600-57284000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
45	chr11:57281800-57283000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr11:57281800-57283200	Active TSS	Gastric	stomach
47	chr11:57281800-57283400	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr11:57281800-57283400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr11:57281800-57283400	Active TSS	Liver	Liver
50	chr11:57281800-57283400	Active TSS	Small Intestine	intestine

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