Variant report

Variant	rs61886978
Chromosome Location	chr11:57194848-57194849
allele	C/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	ELK1	chr11:57194531-57194851	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:57194327-57195045	GM12891	blood:	n/a	n/a
3	POLR2A	chr11:57191261-57195084	K562	blood:	n/a	n/a
4	MAX	chr11:57192105-57195056	NB4	blood:	n/a	chr11:57193991-57194004 chr11:57192303-57192313 chr11:57193410-57193419 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193409-57193420 chr11:57193409-57193420 chr11:57193993-57194003 chr11:57192755-57192766 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57192440-57192449 chr11:57193992-57194001 chr11:57193409-57193420 chr11:57192754-57192769 chr11:57193992-57194003 chr11:57193992-57194003
5	POLR2A	chr11:57191114-57195043	GM12878	blood:	n/a	n/a
6	POLR2A	chr11:57191115-57195177	GM12892	blood:	n/a	n/a
7	MAX	chr11:57191980-57195156	K562	blood:	n/a	chr11:57193991-57194004 chr11:57192303-57192313 chr11:57193410-57193419 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193409-57193420 chr11:57193409-57193420 chr11:57193993-57194003 chr11:57192755-57192766 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57192440-57192449 chr11:57193992-57194001 chr11:57193409-57193420 chr11:57192754-57192769 chr11:57193992-57194003 chr11:57193992-57194003
8	MTA3	chr11:57191526-57195524	GM12878	blood:	n/a	n/a
9	EP300	chr11:57194376-57194884	K562	blood:	n/a	chr11:57194430-57194446
10	E2F6	chr11:57194798-57194960	K562	blood:	n/a	n/a
11	SPI1	chr11:57194541-57194862	HL-60	blood:	n/a	chr11:57194628-57194641
12	POLR2A	chr11:57191591-57194992	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:57193648-57194922	K562	blood:	n/a	n/a
14	POLR2A	chr11:57191113-57195429	HL-60	blood:	n/a	n/a
15	POLR2A	chr11:57194244-57195063	K562	blood:	n/a	n/a
16	NR3C1	chr11:57194830-57195076	A549	lung:	n/a	n/a
17	YY1	chr11:57194244-57195030	K562	blood:	n/a	chr11:57194486-57194500 chr11:57194364-57194373 chr11:57194452-57194466 chr11:57194426-57194440 chr11:57194626-57194640 chr11:57194625-57194634
18	CTCF	chr11:57194780-57194930	HUVEC	blood vessel:	n/a	n/a
19	TAF1	chr11:57194350-57194932	GM12878	blood:	n/a	n/a
20	POLR2A	chr11:57192189-57195457	Raji	blood:	n/a	n/a
21	ELF1	chr11:57194254-57195014	GM12878	blood:	n/a	chr11:57194682-57194695 chr11:57194625-57194634
22	POLR2A	chr11:57194321-57195051	GM10847	blood:	n/a	n/a
23	POLR2A	chr11:57191441-57195068	GM18526	blood:	n/a	n/a
24	TBL1XR1	chr11:57194671-57194942	K562	blood:	n/a	n/a
25	POLR2A	chr11:57194300-57194943	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr11:57193811-57194996	GM12878	blood:	n/a	n/a
27	MYC	chr11:57192097-57195095	NB4	blood:	n/a	chr11:57193991-57194004 chr11:57192303-57192313 chr11:57193410-57193419 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193409-57193420 chr11:57193409-57193420 chr11:57193993-57194003 chr11:57192755-57192766 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57192440-57192449 chr11:57193992-57194001 chr11:57193409-57193420 chr11:57192754-57192769 chr11:57193992-57194003 chr11:57193992-57194003
28	YY1	chr11:57194605-57195071	K562	blood:	n/a	chr11:57194626-57194640 chr11:57194625-57194634
29	POLR2A	chr11:57194421-57194876	HCT-116	colon:	n/a	n/a
30	CHD2	chr11:57194501-57194996	GM12878	blood:	n/a	n/a
31	IRF1	chr11:57194424-57194946	K562	blood:	n/a	chr11:57194624-57194638
32	PML	chr11:57191892-57195093	GM12878	blood:	n/a	chr11:57192441-57192450
33	ELF1	chr11:57194361-57194863	K562	blood:	n/a	chr11:57194682-57194695 chr11:57194625-57194634
34	TBP	chr11:57193796-57194979	GM12878	blood:	n/a	n/a
35	CBX3	chr11:57194402-57195078	K562	blood:	n/a	n/a
36	MTA3	chr11:57194480-57195034	GM12878	blood:	n/a	n/a
37	POLR2A	chr11:57191153-57195123	GM12891	blood:	n/a	n/a
38	CHD2	chr11:57194551-57194889	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr11:57192095-57194977	NB4	blood:	n/a	n/a
40	RUNX3	chr11:57194356-57195208	GM12878	blood:	n/a	n/a
41	RCOR1	chr11:57194375-57195054	K562	blood:	n/a	n/a
42	STAT5A	chr11:57193924-57194919	GM12878	blood:	n/a	chr11:57194601-57194613 chr11:57194607-57194619
43	POLR2A	chr11:57191285-57195328	K562	blood:	n/a	n/a
44	MAX	chr11:57193717-57195177	HCT-116	colon:	n/a	chr11:57193991-57194004 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193993-57194003 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57193992-57194001 chr11:57193992-57194003 chr11:57193992-57194003
45	POLR2A	chr11:57192131-57195018	GM15510	blood:	n/a	n/a
46	RCOR1	chr11:57194153-57194960	GM12878	blood:	n/a	n/a
47	RUNX3	chr11:57192047-57195167	GM12878	blood:	n/a	n/a
48	POLR2A	chr11:57191219-57194857	GM12891	blood:	n/a	n/a
49	MYC	chr11:57192188-57195515	MCF10A-Er-Src	breast:	n/a	chr11:57193991-57194004 chr11:57192303-57192313 chr11:57193410-57193419 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193409-57193420 chr11:57193409-57193420 chr11:57193993-57194003 chr11:57192755-57192766 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57192440-57192449 chr11:57193992-57194001 chr11:57193409-57193420 chr11:57192754-57192769 chr11:57193992-57194003 chr11:57193992-57194003
50	MAX	chr11:57193464-57194850	H1-hESC	embryonic stem cell:	n/a	chr11:57193991-57194004 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193993-57194003 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57193992-57194001 chr11:57193992-57194003 chr11:57193992-57194003

No.	Distal block	Cell Line	Cell type
1	chr11:57194115..57196219-chr11:57423627..57426056,2	K562	blood:
2	chr11:57194137..57194904-chr7:2594523..2595486,2	NB4	blood:
3	chr11:57194318..57196008-chr11:57227438..57230083,2	K562	blood:
4	chr11:57194058..57195845-chr11:57267357..57269723,2	K562	blood:
5	chr11:57094351..57096693-chr11:57193203..57197242,3	K562	blood:

Variant related genes	Relation type
SLC43A3	TF binding region
ENSG00000254979	TF binding region
ENSG00000238692	Chromatin interaction
ENSG00000106009	Chromatin interaction
ENSG00000149150	Chromatin interaction
ENSG00000172409	Chromatin interaction
ENSG00000186907	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11229028	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11820985	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11822095	0.98[ASN][1000 genomes]
rs11822910	0.96[ASN][1000 genomes]
rs11827928	0.96[ASN][1000 genomes]
rs11828218	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12422015	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2250887	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2439448	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2511982	0.84[EUR][1000 genomes]
rs2581924	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2581927	0.86[EUR][1000 genomes]
rs2581928	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2584858	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2729389	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2729392	0.86[EUR][1000 genomes]
rs4477456	0.96[ASN][1000 genomes]
rs4529894	0.96[ASN][1000 genomes]
rs60961847	0.89[ASN][1000 genomes]
rs7106223	0.89[ASN][1000 genomes]
rs7122734	0.91[ASN][1000 genomes]
rs7943531	0.84[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61886978	TIMM10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57191600-57195200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr11:57191600-57195600	Enhancers	Spleen	Spleen
3	chr11:57191800-57195000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr11:57191800-57195000	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr11:57191800-57195000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr11:57191800-57195200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr11:57192000-57195000	Flanking Active TSS	Fetal Thymus	thymus
8	chr11:57192200-57195000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
9	chr11:57192200-57195000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr11:57192200-57195200	Flanking Active TSS	Brain Germinal Matrix	brain
11	chr11:57192200-57195400	Flanking Active TSS	Osteobl	bone
12	chr11:57192400-57195400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr11:57192800-57195000	Flanking Active TSS	NHDF-Ad	bronchial
14	chr11:57192800-57195200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr11:57193000-57195000	Flanking Active TSS	Rectal Smooth Muscle	rectum
16	chr11:57193200-57195600	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr11:57193400-57195000	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr11:57193400-57195000	Flanking Active TSS	HMEC	breast
19	chr11:57193400-57195000	Flanking Active TSS	HUVEC	blood vessel
20	chr11:57193400-57195200	Flanking Active TSS	Fetal Muscle Trunk	muscle
21	chr11:57193600-57195000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:57193600-57195000	Flanking Active TSS	NHEK	skin
23	chr11:57193600-57195000	Flanking Active TSS	NHLF	lung
24	chr11:57193600-57195400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:57193600-57195400	Weak transcription	Small Intestine	intestine
26	chr11:57193800-57195000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:57193800-57195000	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr11:57193800-57195000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr11:57193800-57195000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr11:57193800-57195000	Flanking Active TSS	Fetal Brain Male	brain
31	chr11:57193800-57195000	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr11:57193800-57195200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:57193800-57195400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr11:57194000-57195000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
35	chr11:57194000-57195000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr11:57194000-57195000	Flanking Active TSS	Primary B cells from peripheral blood	blood
37	chr11:57194000-57195000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr11:57194000-57195000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr11:57194000-57195000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr11:57194000-57195000	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr11:57194000-57195000	Active TSS	Ovary	ovary
42	chr11:57194000-57195000	Flanking Active TSS	NH-A	brain
43	chr11:57194000-57195400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr11:57194000-57195400	Active TSS	Aorta	Aorta
45	chr11:57194000-57195400	Flanking Active TSS	HSMMtube	muscle
46	chr11:57194200-57195000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr11:57194200-57195000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr11:57194200-57195000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:57194200-57195000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
50	chr11:57194200-57195000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell

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