Variant report

Variant	rs10024928
Chromosome Location	chr4:56242054-56242055
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	chr4:56240281..56248484-chr4:56258541..56264383,10	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLOCK-1	chr4:56241699-56242139	ENSG00000249700.4

Variant related genes	Relation type
ENSG00000134851	Chromatin interaction
ENSG00000249700	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10010762	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021233	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17776975	0.84[ASN][1000 genomes]
rs1818460	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1818461	0.84[ASN][1000 genomes]
rs1961107	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2538	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28609134	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3087606	0.95[ASN][1000 genomes]
rs4089487	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4455482	1.00[ASN][1000 genomes]
rs475465	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476184	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482114	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs483978	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs496055	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499110	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525271	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs552792	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs552950	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs556072	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56139168	0.84[ASN][1000 genomes]
rs572428	0.95[ASN][1000 genomes]
rs572553	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs573960	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs576732	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58176292	0.88[ASN][1000 genomes]
rs58506276	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59648459	0.91[ASN][1000 genomes]
rs60097207	0.84[ASN][1000 genomes]
rs62303681	0.84[ASN][1000 genomes]
rs62305200	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305201	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62305202	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62305206	0.98[ASN][1000 genomes]
rs62306207	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs693367	0.95[ASN][1000 genomes]
rs819203	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs819266	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs819267	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs819268	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs819269	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs819270	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs861029	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880358	0.84[ASN][1000 genomes]
rs9312660	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56213600-56242600	Weak transcription	Gastric	stomach
2	chr4:56213800-56251400	Weak transcription	Pancreas	Pancrea
3	chr4:56214400-56247600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:56225800-56244800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr4:56225800-56244800	Weak transcription	Stomach Mucosa	stomach
6	chr4:56226000-56245000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr4:56226000-56245000	Weak transcription	HSMMtube	muscle
8	chr4:56228000-56244800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:56228400-56245400	Weak transcription	K562	blood
10	chr4:56228400-56251000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:56230600-56245200	Weak transcription	Fetal Intestine Small	intestine
12	chr4:56232000-56247600	Weak transcription	Spleen	Spleen
13	chr4:56233200-56261600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:56234000-56244800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:56235800-56247600	Weak transcription	Aorta	Aorta
16	chr4:56236400-56242200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr4:56236400-56248400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:56236800-56243800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:56237000-56245400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:56237000-56247800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:56237200-56243200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr4:56237200-56247800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:56239000-56245000	Weak transcription	Adipose Nuclei	Adipose
24	chr4:56239800-56251400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:56240200-56249400	Weak transcription	Left Ventricle	heart
26	chr4:56240400-56242200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:56240400-56243200	Weak transcription	Brain Anterior Caudate	brain
28	chr4:56240400-56243400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr4:56240400-56259600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr4:56240600-56243600	Weak transcription	Brain Substantia Nigra	brain
31	chr4:56240600-56243800	Weak transcription	Brain Hippocampus Middle	brain
32	chr4:56240800-56247400	Weak transcription	Brain Angular Gyrus	brain
33	chr4:56241000-56243200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr4:56241200-56244600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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