Variant report

Variant	rs12510769
Chromosome Location	chr4:3394374-3394375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3386670..3388644-chr4:3392209..3394600,2	MCF-7	breast:
2	chr4:3388256..3390546-chr4:3393263..3395293,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10012797	0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10027926	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12641989	0.85[CHB][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17190954	0.80[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2269496	0.81[CEU][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3088231	0.90[CEU][hapmap];0.90[CHB][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3748037	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73193383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv878463	chr4:3363994-3498896	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv428435	chr4:3386773-3623321	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv933265	chr4:3392824-4283640	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
11	esv2757918	chr4:3394344-4350986	Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
12	esv2759219	chr4:3394344-4350986	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3386800-3395800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:3388000-3394400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:3388600-3394400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:3388800-3394400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr4:3389200-3395000	Weak transcription	HepG2	liver
6	chr4:3389200-3403400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr4:3390000-3404600	Weak transcription	Left Ventricle	heart
8	chr4:3390000-3417200	Weak transcription	Gastric	stomach
9	chr4:3390200-3398600	Weak transcription	Brain Angular Gyrus	brain
10	chr4:3391000-3398000	Weak transcription	Fetal Brain Female	brain
11	chr4:3391000-3404600	Weak transcription	Aorta	Aorta
12	chr4:3391000-3414000	Weak transcription	Primary T cells from cord blood	blood
13	chr4:3391200-3396800	Weak transcription	NHLF	lung
14	chr4:3391200-3398800	Weak transcription	Right Atrium	heart
15	chr4:3391400-3407400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:3391400-3408800	Weak transcription	Ovary	ovary
17	chr4:3391600-3395200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:3391600-3397800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr4:3391600-3399200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:3391600-3404000	Weak transcription	HSMMtube	muscle
21	chr4:3391600-3407800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr4:3391800-3398000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:3391800-3401400	Weak transcription	Liver	Liver
24	chr4:3391800-3403000	Weak transcription	HMEC	breast
25	chr4:3391800-3403400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr4:3391800-3424200	Weak transcription	Colonic Mucosa	Colon
27	chr4:3392000-3395000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr4:3392000-3395000	Weak transcription	GM12878-XiMat	blood
29	chr4:3392000-3396800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:3392000-3398000	Weak transcription	Fetal Lung	lung
31	chr4:3392000-3417200	Weak transcription	Pancreas	Pancrea
32	chr4:3392200-3394400	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr4:3392200-3395000	Weak transcription	Fetal Thymus	thymus
34	chr4:3392200-3397000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:3392400-3395400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr4:3392400-3397800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:3392400-3403200	Weak transcription	Fetal Intestine Small	intestine
38	chr4:3392400-3409800	Weak transcription	Spleen	Spleen
39	chr4:3392600-3394400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:3392600-3394600	Weak transcription	Brain Anterior Caudate	brain
41	chr4:3392600-3395000	Weak transcription	Lung	lung
42	chr4:3392600-3398800	Weak transcription	Esophagus	oesophagus
43	chr4:3392600-3404200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr4:3392800-3394400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:3392800-3395000	Enhancers	HSMM	muscle
46	chr4:3393400-3394600	Weak transcription	Placenta	Placenta
47	chr4:3393400-3395200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr4:3393400-3395400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr4:3393400-3395400	Weak transcription	Fetal Stomach	stomach
50	chr4:3393400-3405400	Weak transcription	Brain Germinal Matrix	brain

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