Variant report

Variant	rs2560258
Chromosome Location	chr5:94843487-94843488
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:94840762..94844216-chr5:94846022..94849276,5	K562	blood:
2	chr5:94835766..94839248-chr5:94841208..94845104,3	K562	blood:
3	chr5:94841082..94843868-chr5:94850976..94852780,2	K562	blood:
4	chr5:94840762..94845764-chr5:94846022..94849276,7	K562	blood:

Variant related genes	Relation type
ENSG00000198677	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10053324	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10076499	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1183640	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1541798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1981952	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2245588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2545841	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2548652	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2560257	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560260	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2560261	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2560274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2731825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2731826	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2731833	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881976	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61270217	0.82[ASN][1000 genomes]
rs6556870	0.92[ASN][1000 genomes]
rs73777211	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9314148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882388	chr5:94764006-94925849	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv598954	chr5:94783175-94859599	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:94811000-94889400	Weak transcription	Stomach Mucosa	stomach
2	chr5:94815400-94853200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:94817200-94849000	Weak transcription	Small Intestine	intestine
4	chr5:94817400-94865600	Strong transcription	Osteobl	bone
5	chr5:94818000-94882400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:94822400-94847800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr5:94824400-94862200	Weak transcription	Colonic Mucosa	Colon
8	chr5:94824800-94843800	Strong transcription	Liver	Liver
9	chr5:94824800-94847200	Weak transcription	Brain Substantia Nigra	brain
10	chr5:94824800-94866000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:94825000-94886200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:94825200-94866000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:94825400-94852200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:94825400-94886400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr5:94826000-94847400	Weak transcription	Fetal Heart	heart
16	chr5:94826000-94886400	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr5:94826800-94886400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr5:94827200-94848800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr5:94827200-94865600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:94827200-94866800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:94827200-94889600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:94827400-94848800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr5:94828000-94847600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr5:94828600-94873600	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr5:94828800-94862600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:94828800-94885800	Strong transcription	Fetal Thymus	thymus
27	chr5:94829000-94844200	Weak transcription	K562	blood
28	chr5:94829200-94866200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:94831400-94868400	Strong transcription	Fetal Intestine Large	intestine
30	chr5:94831600-94856200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:94833200-94847200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:94833200-94848200	Weak transcription	Hela-S3	cervix
33	chr5:94834200-94845000	Weak transcription	HepG2	liver
34	chr5:94835200-94845000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:94835200-94845000	Weak transcription	Aorta	Aorta
36	chr5:94835200-94845000	Weak transcription	Esophagus	oesophagus
37	chr5:94835200-94845000	Weak transcription	Gastric	stomach
38	chr5:94835200-94845000	Weak transcription	Lung	lung
39	chr5:94835200-94845000	Weak transcription	Pancreas	Pancrea
40	chr5:94835200-94846000	Weak transcription	Brain Angular Gyrus	brain
41	chr5:94835200-94847200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr5:94835200-94847800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr5:94835200-94848800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr5:94835200-94864800	Weak transcription	Spleen	Spleen
45	chr5:94835200-94881000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:94835400-94868000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:94836200-94866400	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr5:94836600-94860800	Strong transcription	Placenta	Placenta
49	chr5:94836600-94861000	Strong transcription	Duodenum Mucosa	Duodenum
50	chr5:94836600-94867600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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