Variant report

Variant	rs12222684
Chromosome Location	chr11:9232590-9232591
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:63)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:63 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr11:9232532-9232937	GM12878	blood:	n/a	n/a
2	RELA	chr11:9232525-9233025	GM18951	blood:	n/a	n/a
3	IKZF1	chr11:9232284-9233160	GM12878	blood:	n/a	n/a
4	SPI1	chr11:9232468-9232916	GM12878	blood:	n/a	n/a
5	POU2F2	chr11:9232483-9232964	GM12878	blood:	n/a	n/a
6	BATF	chr11:9232527-9232885	GM12878	blood:	n/a	n/a
7	NFIC	chr11:9232286-9233557	GM12878	blood:	n/a	n/a
8	CEBPB	chr11:9231940-9232750	HCT-116	colon:	n/a	n/a
9	BCLAF1	chr11:9232268-9232948	GM12878	blood:	n/a	n/a
10	BHLHE40	chr11:9232573-9232954	GM12878	blood:	n/a	n/a
11	TCF12	chr11:9232580-9232908	GM12878	blood:	n/a	n/a
12	MEF2A	chr11:9232400-9232939	GM12878	blood:	n/a	n/a
13	SP1	chr11:9232462-9232953	GM12878	blood:	n/a	n/a
14	EBF1	chr11:9232555-9232906	GM12878	blood:	n/a	n/a
15	RUNX3	chr11:9232166-9233500	GM12878	blood:	n/a	n/a
16	PAX5	chr11:9231983-9232939	GM12878	blood:	n/a	n/a
17	STAT3	chr11:9232250-9232822	MCF10A-Er-Src	breast:	n/a	n/a
18	EP300	chr11:9232485-9232980	GM12878	blood:	n/a	n/a
19	RELA	chr11:9232487-9232999	GM10847	blood:	n/a	n/a
20	STAT3	chr11:9232252-9232834	MCF10A-Er-Src	breast:	n/a	n/a
21	RELA	chr11:9232525-9233511	GM18505	blood:	n/a	n/a
22	STAT5A	chr11:9232334-9232957	GM12878	blood:	n/a	n/a
23	NFATC1	chr11:9232423-9233013	GM12878	blood:	n/a	n/a
24	EP300	chr11:9232444-9232941	GM12878	blood:	n/a	n/a
25	ATF2	chr11:9232336-9233237	GM12878	blood:	n/a	n/a
26	RELA	chr11:9232465-9233191	GM12891	blood:	n/a	n/a
27	BCL11A	chr11:9232471-9232866	GM12878	blood:	n/a	n/a
28	CHD1	chr11:9232178-9232890	GM12878	blood:	n/a	n/a
29	CEBPB	chr11:9231873-9232616	A549	lung:	n/a	n/a
30	FOXM1	chr11:9232238-9233090	GM12878	blood:	n/a	n/a
31	IRF4	chr11:9232418-9232981	GM12878	blood:	n/a	n/a
32	STAT3	chr11:9232303-9232814	MCF10A-Er-Src	breast:	n/a	n/a
33	ATF2	chr11:9232373-9233273	GM12878	blood:	n/a	n/a
34	PML	chr11:9232214-9232955	GM12878	blood:	n/a	n/a
35	PAX5	chr11:9232417-9232919	GM12878	blood:	n/a	n/a
36	PBX3	chr11:9232579-9232778	GM12878	blood:	n/a	n/a
37	NFATC1	chr11:9232259-9233266	GM12878	blood:	n/a	n/a
38	RELA	chr11:9232537-9232958	GM15510	blood:	n/a	n/a
39	TBL1XR1	chr11:9232493-9233073	GM12878	blood:	n/a	n/a
40	FOS	chr11:9232364-9232670	MCF10A-Er-Src	breast:	n/a	n/a
41	TCF12	chr11:9232537-9232871	GM12878	blood:	n/a	n/a
42	MTA3	chr11:9232220-9233084	GM12878	blood:	n/a	n/a
43	BATF	chr11:9232434-9233001	GM12878	blood:	n/a	n/a
44	FOXM1	chr11:9232314-9233120	GM12878	blood:	n/a	n/a
45	BCL3	chr11:9232520-9232918	GM12878	blood:	n/a	n/a
46	RELA	chr11:9232385-9233180	GM12878	blood:	n/a	n/a
47	SPI1	chr11:9232474-9232911	GM12891	blood:	n/a	n/a
48	RUNX3	chr11:9232018-9233267	GM12878	blood:	n/a	n/a
49	MTA3	chr11:9231851-9233057	GM12878	blood:	n/a	n/a
50	CEBPB	chr11:9232000-9232661	HCT-116	colon:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9227104..9229511-chr11:9232191..9234529,3	K562	blood:
2	chr11:9223393..9225433-chr11:9231691..9234653,2	K562	blood:

No data

Variant related genes	Relation type
DENND5A	TF binding region
ENSG00000184014	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11042182	0.93[YRI][hapmap]
rs11042221	0.89[EUR][1000 genomes];0.85[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	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040049	chr11:9152536-9363488	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv1053045	chr11:9208881-9363488	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv540947	chr11:9208881-9363488	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12222684	ADM	cis	cerebellum	SCAN
rs12222684	MRPL17	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9169600-9238000	Weak transcription	Esophagus	oesophagus
2	chr11:9202600-9251200	Weak transcription	Small Intestine	intestine
3	chr11:9224000-9232600	Weak transcription	Colonic Mucosa	Colon
4	chr11:9225400-9236800	Weak transcription	Primary B cells from cord blood	blood
5	chr11:9225800-9234400	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr11:9225800-9236200	Weak transcription	Thymus	Thymus
7	chr11:9225800-9237800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr11:9225800-9237800	Weak transcription	Gastric	stomach
9	chr11:9226000-9236400	Weak transcription	Lung	lung
10	chr11:9226000-9236800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr11:9226000-9241200	Weak transcription	Aorta	Aorta
12	chr11:9226000-9252000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:9226000-9252800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr11:9226200-9236200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:9227200-9236600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr11:9227400-9236200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:9227400-9236400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr11:9227400-9250400	Weak transcription	Fetal Stomach	stomach
19	chr11:9227600-9236400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr11:9227600-9250600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr11:9228000-9232600	Enhancers	Brain Cingulate Gyrus	brain
22	chr11:9228400-9232600	Enhancers	Brain Substantia Nigra	brain
23	chr11:9228400-9232800	Enhancers	Brain Anterior Caudate	brain
24	chr11:9228400-9236400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr11:9228400-9236600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr11:9228400-9236600	Weak transcription	HUVEC	blood vessel
27	chr11:9228600-9232800	Enhancers	Brain Hippocampus Middle	brain
28	chr11:9228800-9232800	Enhancers	Fetal Heart	heart
29	chr11:9229000-9233000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr11:9229200-9236400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr11:9229600-9232800	Enhancers	K562	blood
32	chr11:9229800-9232600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr11:9229800-9232800	Enhancers	Primary T cells from cord blood	blood
34	chr11:9229800-9233200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr11:9229800-9235200	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr11:9229800-9237600	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr11:9230000-9232800	Flanking Active TSS	GM12878-XiMat	blood
38	chr11:9230200-9232800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr11:9230200-9232800	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr11:9230200-9235200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr11:9230400-9232800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr11:9230400-9233000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:9230400-9233400	Enhancers	Osteobl	bone
44	chr11:9230400-9253400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:9230600-9232800	Enhancers	NHLF	lung
46	chr11:9230600-9235800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr11:9230800-9232800	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr11:9230800-9233000	Enhancers	NHDF-Ad	bronchial
49	chr11:9230800-9233200	Enhancers	Hela-S3	cervix
50	chr11:9230800-9236600	Weak transcription	Stomach Smooth Muscle	stomach

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