Variant report

Variant	rs4235780
Chromosome Location	chr5:112382793-112382794
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112370113..112371972-chr5:112381574..112383609,2	MCF-7	breast:
2	chr5:112256096..112258647-chr5:112382591..112384818,2	K562	blood:
3	chr5:112381725..112385379-chr5:112386016..112389315,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129625	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12521395	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13185006	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17310536	1.00[AMR][1000 genomes]
rs17311019	1.00[AMR][1000 genomes]
rs17311096	1.00[AMR][1000 genomes]
rs17369487	1.00[AMR][1000 genomes]
rs17370550	0.89[AMR][1000 genomes]
rs4235775	1.00[EUR][1000 genomes]
rs4235776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4235781	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4235782	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4235783	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4235784	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4235785	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4260661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4276396	1.00[EUR][1000 genomes]
rs4295378	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4519915	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4627978	1.00[EUR][1000 genomes]
rs4705534	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4705535	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4705536	1.00[EUR][1000 genomes]
rs4705757	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4705759	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4705760	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4705761	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4705764	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4705765	1.00[EUR][1000 genomes]
rs55901036	1.00[AMR][1000 genomes]
rs55940904	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55997238	0.95[EUR][1000 genomes]
rs56023848	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56265422	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59876839	0.81[AFR][1000 genomes]
rs6594657	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6594658	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6594666	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6594667	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6594668	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6862944	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6872473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6881198	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6881233	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6881426	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6881477	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6882115	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6896675	0.95[EUR][1000 genomes]
rs6897972	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7706745	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7728495	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs878074	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs878075	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv882717	chr5:112336588-112408944	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv15902	chr5:112369563-112410775	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv599395	chr5:112370311-112428869	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv1817377	chr5:112373682-112389837	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv516887	chr5:112379659-112396174	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112362800-112385800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:112363600-112382800	Weak transcription	Fetal Intestine Small	intestine
3	chr5:112363800-112384600	Weak transcription	Aorta	Aorta
4	chr5:112363800-112386200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:112363800-112399000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:112363800-112409200	Weak transcription	Colonic Mucosa	Colon
7	chr5:112363800-112417800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:112364000-112389400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr5:112364200-112386600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr5:112364800-112382800	Weak transcription	Fetal Intestine Large	intestine
11	chr5:112364800-112382800	Weak transcription	Fetal Thymus	thymus
12	chr5:112368800-112382800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr5:112369400-112382800	Strong transcription	Liver	Liver
14	chr5:112370200-112406600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:112370600-112382800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:112370600-112396600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:112371000-112383400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:112371400-112391400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr5:112371400-112423800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:112371600-112394200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:112372600-112384000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:112372800-112396800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr5:112373000-112382800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr5:112373000-112383000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr5:112373000-112398800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr5:112373200-112399000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr5:112374600-112383200	Weak transcription	Fetal Kidney	kidney
28	chr5:112374800-112383200	Weak transcription	Osteobl	bone
29	chr5:112374800-112386000	Weak transcription	NHDF-Ad	bronchial
30	chr5:112374800-112386200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:112375000-112402600	Weak transcription	Pancreas	Pancrea
32	chr5:112375200-112384400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:112377400-112386400	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr5:112377400-112389000	Weak transcription	Primary T cells from cord blood	blood
35	chr5:112378200-112383000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:112379200-112382800	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr5:112379400-112383000	Weak transcription	HUVEC	blood vessel
38	chr5:112379400-112383000	Enhancers	K562	blood
39	chr5:112379600-112382800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr5:112379600-112386400	Weak transcription	Brain Angular Gyrus	brain
41	chr5:112379600-112386400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr5:112379600-112388800	Weak transcription	Gastric	stomach
43	chr5:112379600-112388800	Weak transcription	Spleen	Spleen
44	chr5:112379600-112399600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr5:112379600-112424200	Weak transcription	Psoas Muscle	Psoas
46	chr5:112379800-112382800	Weak transcription	Brain Hippocampus Middle	brain
47	chr5:112379800-112384800	Genic enhancers	Ovary	ovary
48	chr5:112379800-112386200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr5:112379800-112386400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr5:112379800-112388800	Weak transcription	Brain Substantia Nigra	brain

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