Variant report

Variant	rs55968289
Chromosome Location	chr3:139260285-139260286
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:139254870-139260531	SK-N-SH	brain:	n/a	n/a
2	KAP1	chr3:139259464-139260440	U2OS	brain:	n/a	n/a
3	KAP1	chr3:139259465-139260908	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:139251954..139254660-chr3:139259598..139262357,2	MCF-7	breast:
2	chr3:139259982..139261816-chr3:139261928..139264277,2	K562	blood:
3	chr3:139259820..139261724-chr3:139263779..139266095,2	MCF-7	breast:

Variant related genes	Relation type
RBP1	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1116748	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11549984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489687	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493507	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1391029	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1391030	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1391031	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511570	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511571	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17337746	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17397112	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011770	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772868	0.93[EUR][1000 genomes]
rs3821543	0.93[EUR][1000 genomes]
rs4270469	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4407373	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683502	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs55641400	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55642746	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55724241	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55780517	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55817881	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55834130	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55987999	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56034427	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56051054	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56051514	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56058641	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56170893	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56210757	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56343214	0.93[EUR][1000 genomes]
rs57459746	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220932	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220940	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220941	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220944	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220945	0.97[ASN][1000 genomes]
rs893703	0.93[EUR][1000 genomes]
rs930412	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer 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	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139259000-139260400	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr3:139259200-139260400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:139259200-139260800	Enhancers	Brain Angular Gyrus	brain
4	chr3:139259200-139261000	Enhancers	Brain Cingulate Gyrus	brain
5	chr3:139259200-139307000	Weak transcription	Aorta	Aorta
6	chr3:139259400-139260600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:139259400-139260800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
8	chr3:139259400-139261200	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr3:139259600-139260600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:139259600-139260800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:139259600-139260800	Flanking Active TSS	Brain Germinal Matrix	brain
12	chr3:139259600-139260800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:139259600-139260800	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr3:139259600-139261200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:139259600-139261200	Enhancers	Right Atrium	heart
16	chr3:139259800-139260400	Enhancers	Fetal Brain Male	brain
17	chr3:139259800-139260600	Enhancers	Esophagus	oesophagus
18	chr3:139259800-139260600	Flanking Active TSS	Ovary	ovary
19	chr3:139259800-139260600	Flanking Active TSS	Pancreas	Pancrea
20	chr3:139259800-139260600	Enhancers	Right Ventricle	heart
21	chr3:139259800-139260600	Enhancers	Stomach Smooth Muscle	stomach
22	chr3:139259800-139260600	Enhancers	Spleen	Spleen
23	chr3:139259800-139260800	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr3:139259800-139260800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
25	chr3:139259800-139261600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:139259800-139261800	Enhancers	Fetal Stomach	stomach
27	chr3:139260000-139260400	Enhancers	Fetal Heart	heart
28	chr3:139260000-139260600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:139260000-139260600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
30	chr3:139260000-139260600	Enhancers	Fetal Intestine Small	intestine
31	chr3:139260000-139260800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
32	chr3:139260000-139260800	Weak transcription	HMEC	breast
33	chr3:139260000-139261000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:139260000-139261000	Enhancers	Brain Anterior Caudate	brain
35	chr3:139260000-139261200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr3:139260000-139261200	Enhancers	Brain Substantia Nigra	brain
37	chr3:139260200-139260400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
38	chr3:139260200-139260400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:139260200-139260400	Flanking Active TSS	Brain Hippocampus Middle	brain
40	chr3:139260200-139260400	Enhancers	HSMMtube	muscle
41	chr3:139260200-139260600	Enhancers	Fetal Kidney	kidney
42	chr3:139260200-139260800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:139260200-139260800	Enhancers	NH-A	brain
44	chr3:139260200-139261200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
45	chr3:139260200-139261200	Enhancers	Fetal Lung	lung
46	chr3:139260200-139262000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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