Variant report

Variant	rs623083
Chromosome Location	chr5:43076282-43076283
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:43073445..43076704-chr5:43084817..43087387,3	K562	blood:
2	chr5:43074046..43076584-chr5:43103613..43105462,2	K562	blood:
3	chr5:43038312..43041170-chr5:43074041..43076906,4	K562	blood:
4	chr5:43036891..43039253-chr5:43074561..43077276,2	MCF-7	breast:
5	chr5:43073926..43078603-chr5:43119856..43123275,4	K562	blood:
6	chr5:43074312..43077357-chr5:43077925..43083201,8	K562	blood:
7	chr5:43074261..43076510-chr5:43094818..43096635,2	K562	blood:
8	chr5:43061551..43063587-chr5:43074317..43077057,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC114947.1.1-2	chr5:43071269-43076732	XLOC_004366
2	lnc-C5orf39-1	chr5:43076242-43076776	NONHSAT101278

No data

Variant related genes	Relation type
ENSG00000172262	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1690989	1.00[AMR][1000 genomes]
rs1690996	1.00[AMR][1000 genomes]
rs2444778	1.00[AMR][1000 genomes]
rs2453311	1.00[AMR][1000 genomes]
rs2548375	1.00[AMR][1000 genomes]
rs309941	1.00[AMR][1000 genomes]
rs4549536	1.00[AMR][1000 genomes]
rs473870	1.00[AMR][1000 genomes]
rs481347	1.00[AMR][1000 genomes]
rs482224	1.00[AMR][1000 genomes]
rs4866731	1.00[AMR][1000 genomes]
rs500322	1.00[AMR][1000 genomes]
rs500993	1.00[AMR][1000 genomes]
rs516939	1.00[AMR][1000 genomes]
rs534655	1.00[AMR][1000 genomes]
rs549343	1.00[AMR][1000 genomes]
rs550847	1.00[AMR][1000 genomes]
rs558935	1.00[AMR][1000 genomes]
rs566582	1.00[AMR][1000 genomes]
rs6414901	1.00[AMR][1000 genomes]
rs661413	1.00[AMR][1000 genomes]
rs665790	1.00[AMR][1000 genomes]
rs666663	1.00[AMR][1000 genomes]
rs6888146	1.00[AMR][1000 genomes]
rs693466	1.00[AMR][1000 genomes]
rs73090731	1.00[AMR][1000 genomes]
rs7712183	1.00[AMR][1000 genomes]
rs7727600	1.00[AMR][1000 genomes]
rs782973	1.00[AMR][1000 genomes]
rs782981	1.00[AMR][1000 genomes]
rs782982	1.00[AMR][1000 genomes]
rs782983	1.00[AMR][1000 genomes]
rs782986	1.00[AMR][1000 genomes]
rs803501	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription 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	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
7	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking 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	283 gene(s)	inside rSNPs	diseases
8	nsv870299	chr5:43053679-43107880	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43068000-43077600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:43068600-43082600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr5:43069000-43081400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:43069400-43082800	Weak transcription	Colonic Mucosa	Colon
5	chr5:43069400-43087400	Weak transcription	Stomach Mucosa	stomach
6	chr5:43069600-43077000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:43069600-43080400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr5:43069600-43080400	Strong transcription	Fetal Muscle Leg	muscle
9	chr5:43070000-43105400	Weak transcription	HSMMtube	muscle
10	chr5:43070200-43077600	Strong transcription	Fetal Intestine Small	intestine
11	chr5:43071400-43084400	Weak transcription	Fetal Kidney	kidney
12	chr5:43071600-43079000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:43071600-43079000	Weak transcription	NH-A	brain
14	chr5:43071600-43080800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr5:43071600-43083800	Weak transcription	HepG2	liver
16	chr5:43071600-43084200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:43071800-43076800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr5:43071800-43077600	Weak transcription	A549	lung
19	chr5:43071800-43079000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:43071800-43079600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr5:43071800-43080000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr5:43071800-43080000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr5:43071800-43080200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr5:43071800-43080200	Weak transcription	Gastric	stomach
25	chr5:43071800-43081400	Weak transcription	Fetal Brain Male	brain
26	chr5:43071800-43081800	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr5:43071800-43081800	Weak transcription	Hela-S3	cervix
28	chr5:43071800-43082000	Weak transcription	HMEC	breast
29	chr5:43071800-43082800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr5:43071800-43083000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr5:43071800-43084800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:43071800-43091000	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:43071800-43091600	Weak transcription	Ovary	ovary
34	chr5:43071800-43096000	Weak transcription	Aorta	Aorta
35	chr5:43071800-43098400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr5:43071800-43101600	Weak transcription	Esophagus	oesophagus
37	chr5:43071800-43105400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr5:43072000-43079800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr5:43072000-43080600	Weak transcription	Brain Substantia Nigra	brain
40	chr5:43072000-43081800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr5:43072200-43077200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr5:43072400-43077000	Weak transcription	Liver	Liver
43	chr5:43072400-43077200	Weak transcription	Primary T cells from cord blood	blood
44	chr5:43072400-43104200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr5:43072800-43076800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr5:43073000-43080400	Weak transcription	HSMM	muscle
47	chr5:43073400-43079800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr5:43073400-43080400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:43074000-43078600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr5:43074000-43082600	Strong transcription	Fetal Thymus	thymus

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