Variant report

Variant	rs57904538
Chromosome Location	chr4:3289608-3289609
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3287264..3290154-chr4:3470213..3472155,2	MCF-7	breast:
2	chr4:3276746..3278804-chr4:3288196..3290777,2	K562	blood:
3	chr4:3285178..3287998-chr4:3288416..3291256,2	K562	blood:
4	chr4:3272762..3274789-chr4:3288374..3291256,2	MCF-7	breast:
5	chr4:3287370..3290195-chr4:3296120..3298356,2	K562	blood:
6	chr4:3288141..3289800-chr4:3461769..3463366,2	MCF-7	breast:
7	chr4:3245063..3247633-chr4:3289230..3291965,2	MCF-7	breast:
8	chr4:3289451..3291897-chr4:3292555..3295827,4	K562	blood:

Variant related genes	Relation type
ENSG00000188981	Chromatin interaction
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1120898	1.00[ASN][1000 genomes]
rs13110866	0.91[ASN][1000 genomes]
rs13120043	0.91[ASN][1000 genomes]
rs13126960	0.91[ASN][1000 genomes]
rs13129052	0.91[ASN][1000 genomes]
rs13130998	0.91[ASN][1000 genomes]
rs13133859	0.91[ASN][1000 genomes]
rs13150521	1.00[ASN][1000 genomes]
rs16844124	0.91[ASN][1000 genomes]
rs16844147	1.00[ASN][1000 genomes]
rs16844152	1.00[ASN][1000 genomes]
rs34004517	0.91[ASN][1000 genomes]
rs34052318	0.91[ASN][1000 genomes]
rs34067673	1.00[ASN][1000 genomes]
rs34628563	0.91[ASN][1000 genomes]
rs34780636	0.91[ASN][1000 genomes]
rs34849917	0.91[ASN][1000 genomes]
rs35150150	1.00[ASN][1000 genomes]
rs35450001	0.91[ASN][1000 genomes]
rs35720136	0.91[ASN][1000 genomes]
rs35825779	1.00[ASN][1000 genomes]
rs61211078	1.00[ASN][1000 genomes]
rs61748736	0.91[ASN][1000 genomes]
rs71608266	1.00[ASN][1000 genomes]
rs71608267	0.91[ASN][1000 genomes]
rs71608268	0.91[ASN][1000 genomes]
rs71608278	0.91[ASN][1000 genomes]
rs878004	0.90[ASN][1000 genomes]
rs994425	1.00[ASN][1000 genomes]
rs994426	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv878454	chr4:3215835-3305739	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS 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	10 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv878458	chr4:3235518-3303976	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv878459	chr4:3235518-3310831	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
10	nsv878460	chr4:3260154-3303976	Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv878461	chr4:3270488-3339038	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	nsv593440	chr4:3283422-3339038	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
13	nsv461165	chr4:3283422-3342137	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
14	nsv593441	chr4:3283422-3342137	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3286200-3292200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:3286800-3290600	Enhancers	Fetal Brain Male	brain
3	chr4:3287000-3290200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr4:3287000-3290800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr4:3287600-3289800	Enhancers	Ovary	ovary
6	chr4:3287600-3290000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr4:3287600-3290200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:3287600-3290400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:3287600-3290400	Bivalent Enhancer	Fetal Muscle Leg	muscle
10	chr4:3287600-3291000	Enhancers	Brain Germinal Matrix	brain
11	chr4:3287800-3290200	Enhancers	Fetal Brain Female	brain
12	chr4:3288000-3290600	Bivalent Enhancer	Adipose Nuclei	Adipose
13	chr4:3288000-3293200	Weak transcription	Brain Substantia Nigra	brain
14	chr4:3288200-3293200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr4:3288400-3292400	Weak transcription	Pancreas	Pancrea
16	chr4:3288400-3293000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr4:3288600-3289800	Weak transcription	Spleen	Spleen
18	chr4:3288600-3291000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:3288600-3292200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:3288600-3292600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:3288600-3293200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:3288600-3293200	Weak transcription	Brain Anterior Caudate	brain
23	chr4:3288800-3290400	Enhancers	Brain Cingulate Gyrus	brain
24	chr4:3288800-3292600	Weak transcription	HMEC	breast
25	chr4:3289000-3290400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:3289200-3289800	Flanking Active TSS	HepG2	liver
27	chr4:3289200-3292400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:3289200-3292600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr4:3289400-3293000	Weak transcription	Brain Angular Gyrus	brain
30	chr4:3289600-3289800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:3289600-3290200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr4:3289600-3290800	Enhancers	Left Ventricle	heart
33	chr4:3289600-3291200	Enhancers	Lung	lung
34	chr4:3289600-3293200	Weak transcription	Brain Hippocampus Middle	brain
35	chr4:3289600-3293200	Weak transcription	Fetal Lung	lung

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