Variant report

Variant	rs12511823
Chromosome Location	chr4:2944336-2944337
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:79)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:79 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:2943761-2945347	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:2941900-2945918	U87	brain:	n/a	n/a
3	POLR2A	chr4:2943761-2945107	NB4	blood:	n/a	n/a
4	POLR2A	chr4:2944115-2945201	HCT-116	colon:	n/a	n/a
5	MTA3	chr4:2943619-2945276	GM12878	blood:	n/a	n/a
6	POLR2A	chr4:2940251-2945411	MCF-7	breast:	n/a	n/a
7	POLR2A	chr4:2940550-2945810	K562	blood:	n/a	n/a
8	MYC	chr4:2944316-2944524	NB4	blood:	n/a	chr4:2944344-2944354
9	POLR2A	chr4:2941958-2944813	U87	brain:	n/a	n/a
10	POLR2A	chr4:2942195-2945266	GM15510	blood:	n/a	n/a
11	POLR2A	chr4:2943709-2945431	GM12878	blood:	n/a	n/a
12	POLR2A	chr4:2944046-2945207	GM18526	blood:	n/a	n/a
13	POLR2A	chr4:2944199-2945200	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr4:2944066-2944349	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr4:2943815-2945121	A549	lung:	n/a	n/a
16	POLR2A	chr4:2940443-2946234	GM12892	blood:	n/a	n/a
17	POLR2A	chr4:2940559-2945452	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr4:2940564-2945754	HL-60	blood:	n/a	n/a
19	POLR2A	chr4:2943923-2945074	PBDE	blood:	n/a	n/a
20	POLR2A	chr4:2940541-2945723	GM12892	blood:	n/a	n/a
21	POLR2A	chr4:2943823-2945359	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr4:2940925-2945690	GM12878	blood:	n/a	n/a
23	POLR2A	chr4:2943798-2945177	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr4:2942167-2946142	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr4:2940667-2945696	K562	blood:	n/a	n/a
26	POLR2A	chr4:2936437-2945444	GM12892	blood:	n/a	n/a
27	POLR2A	chr4:2940661-2944919	K562	blood:	n/a	n/a
28	POLR2A	chr4:2940303-2945445	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr4:2940538-2945308	GM12891	blood:	n/a	n/a
30	POLR2A	chr4:2944196-2945286	K562	blood:	n/a	n/a
31	POLR2A	chr4:2940169-2946206	GM12892	blood:	n/a	n/a
32	POLR2A	chr4:2940421-2946090	GM18505	blood:	n/a	n/a
33	POLR2A	chr4:2944200-2944988	A549	lung:	n/a	n/a
34	POLR2A	chr4:2942238-2944963	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr4:2940394-2946126	GM12878	blood:	n/a	n/a
36	POLR2A	chr4:2940578-2945412	ECC-1	luminal epithelium:	n/a	n/a
37	PBX3	chr4:2944330-2945278	SK-N-SH	brain:	n/a	chr4:2945232-2945252
38	POLR2A	chr4:2943848-2945337	HCT-116	colon:	n/a	n/a
39	PML	chr4:2944299-2944763	GM12878	blood:	n/a	n/a
40	POLR2A	chr4:2941064-2945424	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr4:2936414-2946052	SK-N-MC	brain:	n/a	n/a
42	ELF1	chr4:2943908-2944541	GM12878	blood:	n/a	n/a
43	POLR2A	chr4:2940245-2946157	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr4:2940527-2945354	GM12891	blood:	n/a	n/a
45	POLR2A	chr4:2941532-2946034	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr4:2940108-2945313	HL-60	blood:	n/a	n/a
47	POLR2A	chr4:2944114-2945116	GM12878	blood:	n/a	n/a
48	POLR2A	chr4:2940267-2946154	K562	blood:	n/a	n/a
49	POLR2A	chr4:2944304-2944431	A549	lung:	n/a	n/a
50	POLR2A	chr4:2940134-2945737	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:2768374..2770834-chr4:2944178..2947093,2	MCF-7	breast:
2	chr3:22963977..22966878-chr4:2943742..2946615,2	MCF-7	breast:
3	chr4:2790052..2809152-chr4:2930639..2948075,83	MCF-7	breast:
4	chr4:2943953..2946628-chr4:2962400..2965288,3	MCF-7	breast:
5	chr4:2914761..2916351-chr4:2943871..2946049,2	K562	blood:

No data

Variant related genes	Relation type
NOP14	TF binding region
ENSG00000087266	Chromatin interaction
ENSG00000087269	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1063744	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12503961	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665452	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7667661	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2937800-2945800	Weak transcription	Fetal Kidney	kidney
2	chr4:2938000-2945400	Genic enhancers	Primary T cells fromperipheralblood	blood
3	chr4:2938000-2960400	Weak transcription	Right Atrium	heart
4	chr4:2938200-2946800	Strong transcription	Thymus	Thymus
5	chr4:2938200-2948400	Strong transcription	Fetal Intestine Small	intestine
6	chr4:2938200-2962200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:2938400-2944400	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:2938400-2957600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:2938400-2959600	Strong transcription	Brain Anterior Caudate	brain
10	chr4:2938400-2962200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:2938600-2949600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:2938600-2960400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:2938600-2960400	Strong transcription	Brain Cingulate Gyrus	brain
14	chr4:2938600-2961000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:2938600-2961600	Strong transcription	Primary T cells from cord blood	blood
16	chr4:2938600-2961600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:2938800-2955600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:2938800-2956800	Strong transcription	Fetal Intestine Large	intestine
19	chr4:2938800-2959200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:2938800-2961000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr4:2938800-2961000	Strong transcription	Primary hematopoietic stem cells	blood
22	chr4:2938800-2961000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:2939000-2956800	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr4:2939000-2956800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr4:2939000-2957400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:2939000-2958400	Strong transcription	Brain Substantia Nigra	brain
27	chr4:2939000-2960200	Strong transcription	Lung	lung
28	chr4:2939000-2961600	Strong transcription	Fetal Stomach	stomach
29	chr4:2939200-2953800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:2939200-2956200	Strong transcription	Left Ventricle	heart
31	chr4:2939200-2959200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:2939200-2959600	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr4:2939200-2960000	Strong transcription	Stomach Smooth Muscle	stomach
34	chr4:2939200-2960600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr4:2939200-2961000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr4:2939200-2963200	Weak transcription	Fetal Heart	heart
37	chr4:2939400-2945800	Strong transcription	HSMMtube	muscle
38	chr4:2939400-2948000	Strong transcription	Liver	Liver
39	chr4:2939400-2952600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:2939400-2956800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:2939400-2957200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:2939400-2959000	Strong transcription	Ovary	ovary
43	chr4:2939400-2959400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:2939400-2959600	Strong transcription	Adipose Nuclei	Adipose
45	chr4:2939400-2959600	Strong transcription	HUVEC	blood vessel
46	chr4:2939400-2959800	Strong transcription	Fetal Muscle Leg	muscle
47	chr4:2939400-2960000	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr4:2939400-2960400	Strong transcription	Fetal Muscle Trunk	muscle
49	chr4:2939400-2960400	Strong transcription	NHLF	lung
50	chr4:2939400-2960600	Strong transcription	Brain Hippocampus Middle	brain

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