Variant report

Variant	rs16844277
Chromosome Location	chr4:3404052-3404053
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3403927..3406519-chr4:3415775..3417384,2	MCF-7	breast:
2	chr4:3403449..3406245-chr4:3407590..3409383,2	K562	blood:
3	chr4:3402342..3405692-chr4:3412930..3417248,3	K562	blood:
4	chr4:3402341..3405091-chr4:3416697..3418981,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10022329	1.00[JPT][hapmap]
rs11942127	1.00[JPT][hapmap]
rs11943410	1.00[JPT][hapmap]
rs1203110	1.00[JPT][hapmap]
rs13128489	1.00[JPT][hapmap]
rs13434660	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843151	1.00[JPT][hapmap]
rs16844209	1.00[JPT][hapmap]
rs16844254	0.92[ASW][hapmap]
rs16844266	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16844272	0.92[ASW][hapmap]
rs16844274	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844282	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16844333	0.82[EUR][1000 genomes]
rs16844345	1.00[JPT][hapmap]
rs2498323	1.00[JPT][hapmap]
rs28444642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28525039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28532840	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28608121	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55901561	0.89[AFR][1000 genomes]
rs60881721	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6813597	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73792007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73792010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73792028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73795536	0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs73795545	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73795547	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3390000-3404600	Weak transcription	Left Ventricle	heart
2	chr4:3390000-3417200	Weak transcription	Gastric	stomach
3	chr4:3391000-3404600	Weak transcription	Aorta	Aorta
4	chr4:3391000-3414000	Weak transcription	Primary T cells from cord blood	blood
5	chr4:3391400-3407400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:3391400-3408800	Weak transcription	Ovary	ovary
7	chr4:3391600-3407800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:3391800-3424200	Weak transcription	Colonic Mucosa	Colon
9	chr4:3392000-3417200	Weak transcription	Pancreas	Pancrea
10	chr4:3392400-3409800	Weak transcription	Spleen	Spleen
11	chr4:3392600-3404200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:3393400-3405400	Weak transcription	Brain Germinal Matrix	brain
13	chr4:3393800-3405600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:3394600-3405400	Weak transcription	Fetal Muscle Leg	muscle
15	chr4:3395800-3406000	Weak transcription	HepG2	liver
16	chr4:3396000-3406000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr4:3398400-3405600	Weak transcription	Fetal Brain Female	brain
18	chr4:3398400-3405800	Weak transcription	Fetal Lung	lung
19	chr4:3399000-3406200	Weak transcription	Adipose Nuclei	Adipose
20	chr4:3399200-3408800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr4:3399200-3432200	Weak transcription	Right Atrium	heart
22	chr4:3401400-3405600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:3401600-3416200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:3401800-3404200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:3401800-3404200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr4:3401800-3406200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:3401800-3407800	Weak transcription	Liver	Liver
28	chr4:3401800-3416000	Weak transcription	Right Ventricle	heart
29	chr4:3402000-3408200	Weak transcription	Brain Anterior Caudate	brain
30	chr4:3402800-3404200	Enhancers	Osteobl	bone
31	chr4:3403000-3405200	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr4:3403000-3405200	Strong transcription	HMEC	breast
33	chr4:3403000-3405800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:3403200-3404200	Enhancers	HSMM	muscle
35	chr4:3403200-3404800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:3403200-3404800	Strong transcription	Fetal Intestine Small	intestine
37	chr4:3403200-3405200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:3403200-3405200	Enhancers	NH-A	brain
39	chr4:3403200-3405200	Enhancers	NHDF-Ad	bronchial
40	chr4:3403200-3406000	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr4:3403200-3406200	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr4:3403200-3409200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr4:3403400-3404400	Strong transcription	Fetal Muscle Trunk	muscle
44	chr4:3403400-3404400	Strong transcription	Fetal Stomach	stomach
45	chr4:3403400-3404800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:3403400-3405200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:3403400-3405200	Enhancers	Muscle Satellite Cultured Cells	--
48	chr4:3403400-3417200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr4:3403600-3404600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:3403600-3405000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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