Variant report

Variant	rs12286249
Chromosome Location	chr11:64215730-64215731
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	RUNX3	chr11:64215516-64216049	GM12878	blood:	n/a	n/a
2	MTA3	chr11:64215446-64216544	GM12878	blood:	n/a	n/a
3	TBL1XR1	chr11:64215673-64215955	GM12878	blood:	n/a	n/a
4	MYC	chr11:64215514-64216647	NB4	blood:	n/a	chr11:64215915-64215925 chr11:64216487-64216497
5	SMC3	chr11:64215714-64216660	GM12878	blood:	n/a	chr11:64216456-64216470
6	CUX1	chr11:64215647-64215968	GM12878	blood:	n/a	n/a
7	CTCF	chr11:64215660-64215810	AG10803	skin:	n/a	n/a
8	MAX	chr11:64215549-64216659	NB4	blood:	n/a	chr11:64215915-64215925 chr11:64216487-64216497
9	CTCF	chr11:64215700-64215850	NHDF-neo	bronchial:	n/a	n/a
10	SPI1	chr11:64215655-64215918	GM12878	blood:	n/a	n/a
11	RAD21	chr11:64215531-64217509	SK-N-SH	brain:	n/a	chr11:64216456-64216470 chr11:64216526-64216539 chr11:64216457-64216464 chr11:64216549-64216561 chr11:64216455-64216474
12	CTCF	chr11:64215700-64215850	WI-38	lung:	n/a	n/a
13	SPI1	chr11:64215213-64216215	HL-60	blood:	n/a	n/a
14	CTCF	chr11:64215620-64215770	HCPEpiC	choroid plexus:	n/a	n/a
15	EP300	chr11:64215597-64216011	GM12878	blood:	n/a	chr11:64215818-64215832
16	FOXA1	chr11:64215332-64215752	T-47D	breast:	n/a	n/a
17	WRNIP1	chr11:64215645-64215833	GM12878	blood:	n/a	n/a
18	BCLAF1	chr11:64215570-64216119	GM12878	blood:	n/a	chr11:64215823-64215832
19	CTCF	chr11:64215720-64215870	HVMF	connective:	n/a	n/a
20	RUNX3	chr11:64215347-64216233	GM12878	blood:	n/a	n/a
21	REST	chr11:64215275-64216659	HL-60	blood:	n/a	chr11:64216322-64216335
22	IRF4	chr11:64215578-64216155	GM12878	blood:	n/a	chr11:64215762-64215776
23	IRF4	chr11:64215637-64216082	GM12878	blood:	n/a	chr11:64215762-64215776
24	REST	chr11:64215689-64215923	Hela-S3	cervix:	n/a	n/a
25	STAT5A	chr11:64215610-64216630	GM12878	blood:	n/a	chr11:64216063-64216075 chr11:64216065-64216077 chr11:64216279-64216291 chr11:64215764-64215775
26	SP1	chr11:64215445-64216049	GM12878	blood:	n/a	chr11:64216000-64216014 chr11:64215999-64216011 chr11:64216001-64216010
27	POLR2A	chr11:64215197-64216780	HL-60	blood:	n/a	n/a
28	CTCF	chr11:64215680-64215830	GM12872	blood:	n/a	n/a
29	CTCF	chr11:64215640-64215790	BJ	skin:	n/a	n/a
30	POLR2A	chr11:64215285-64216707	HL-60	blood:	n/a	n/a
31	MXI1	chr11:64215675-64215899	GM12878	blood:	n/a	n/a
32	IKZF1	chr11:64215462-64216083	GM12878	blood:	n/a	n/a
33	EP300	chr11:64215639-64215945	GM12878	blood:	n/a	chr11:64215818-64215832
34	NFIC	chr11:64215570-64216013	GM12878	blood:	n/a	n/a
35	STAT3	chr11:64215639-64215948	GM12878	blood:	n/a	chr11:64215764-64215775
36	CHD2	chr11:64215714-64216580	GM12878	blood:	n/a	n/a
37	SPI1	chr11:64215528-64216090	HL-60	blood:	n/a	n/a
38	CTCF	chr11:64215720-64215870	NHLF	lung:	n/a	n/a
39	SPI1	chr11:64215555-64216047	GM12878	blood:	n/a	n/a
40	SPI1	chr11:64215537-64216056	GM12891	blood:	n/a	n/a
41	CTCF	chr11:64215620-64215770	AG04450	lung:	n/a	n/a
42	CTCF	chr11:64215700-64215850	GM12864	blood:	n/a	n/a
43	SPI1	chr11:64215516-64216068	GM12891	blood:	n/a	n/a
44	ATF2	chr11:64215551-64216060	GM12878	blood:	n/a	n/a
45	SPI1	chr11:64215392-64216310	GM12878	blood:	n/a	n/a
46	SP1	chr11:64215443-64216061	GM12878	blood:	n/a	chr11:64216000-64216014 chr11:64215999-64216011 chr11:64216001-64216010
47	BHLHE40	chr11:64215708-64216095	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:64206783..64209244-chr11:64213873..64216195,3	K562	blood:
2	chr11:64125330..64128537-chr11:64215213..64218115,3	MCF-7	breast:
3	chr11:64215501..64216385-chr11:64257036..64257826,2	K562	blood:
4	chr11:64071995..64074529-chr11:64215478..64217997,2	K562	blood:

Variant related genes	Relation type
ENSG00000181908	TF binding region
ENSG00000173153	Chromatin interaction
ENSG00000162302	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs539810	0.82[ASN][1000 genomes]
rs59817450	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60200610	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60630604	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832187	chr11:64121969-64312300	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv555194	chr11:64189110-64238023	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64208400-64215800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:64209800-64215800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:64210600-64216200	Weak transcription	Right Atrium	heart
4	chr11:64212800-64216000	Weak transcription	Spleen	Spleen
5	chr11:64213000-64215800	Weak transcription	Brain Substantia Nigra	brain
6	chr11:64215000-64218200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr11:64215200-64215800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:64215200-64215800	Active TSS	Colonic Mucosa	Colon
9	chr11:64215200-64215800	Active TSS	Colon Smooth Muscle	Colon
10	chr11:64215200-64216000	Active TSS	Brain Cingulate Gyrus	brain
11	chr11:64215200-64216000	Enhancers	Placenta	Placenta
12	chr11:64215200-64216200	Enhancers	Brain Angular Gyrus	brain
13	chr11:64215200-64216200	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr11:64215200-64216400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr11:64215200-64216400	Bivalent Enhancer	NH-A	brain
16	chr11:64215200-64216800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:64215200-64216800	Active TSS	Aorta	Aorta
18	chr11:64215200-64217000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:64215200-64217000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr11:64215200-64217200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:64215200-64217200	Flanking Active TSS	Liver	Liver
22	chr11:64215200-64217400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:64215200-64217400	Flanking Active TSS	Fetal Brain Female	brain
24	chr11:64215200-64217600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr11:64215200-64217600	Enhancers	Fetal Brain Male	brain
26	chr11:64215400-64215800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
27	chr11:64215400-64215800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr11:64215400-64215800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
29	chr11:64215400-64215800	Active TSS	Brain Hippocampus Middle	brain
30	chr11:64215400-64215800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
31	chr11:64215400-64215800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
32	chr11:64215400-64215800	Bivalent/Poised TSS	NHDF-Ad	bronchial
33	chr11:64215400-64216000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:64215400-64216000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr11:64215400-64216000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
36	chr11:64215400-64216200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
37	chr11:64215400-64216200	Bivalent Enhancer	Fetal Intestine Large	intestine
38	chr11:64215400-64216200	Flanking Bivalent TSS/Enh	NHLF	lung
39	chr11:64215400-64216400	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr11:64215400-64216400	Bivalent Enhancer	Fetal Stomach	stomach
41	chr11:64215400-64217000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr11:64215400-64217200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr11:64215400-64217200	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr11:64215400-64217200	Flanking Active TSS	Primary B cells from peripheral blood	blood
45	chr11:64215400-64217200	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr11:64215400-64217200	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr11:64215400-64217200	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr11:64215400-64217200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr11:64215400-64217400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr11:64215400-64217400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin

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