Variant report

Variant	rs2282457
Chromosome Location	chr10:5727323-5727324
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:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:5487811..5491565-chr10:5724124..5727399,4	K562	blood:
2	chr10:5486978..5493668-chr10:5725151..5730020,10	MCF-7	breast:
3	chr10:5673035..5675364-chr10:5725053..5728516,4	MCF-7	breast:
4	chr10:5487109..5491565-chr10:5723765..5727399,5	K562	blood:
5	chr10:5673292..5677112-chr10:5724421..5727333,4	K562	blood:
6	chr10:5725239..5729489-chr10:5854026..5858186,8	K562	blood:
7	chr10:5725582..5728827-chr10:5752793..5758658,6	MCF-7	breast:
8	chr10:5487977..5491757-chr10:5726753..5729135,3	MCF-7	breast:
9	chr10:5726952..5729225-chr10:5806393..5808626,2	MCF-7	breast:
10	chr10:5725704..5728346-chr3:33480193..33482855,3	MCF-7	breast:
11	chr10:5706894..5712025-chr10:5724987..5728504,7	MCF-7	breast:
12	chr10:5725559..5728313-chr10:5930802..5933492,3	K562	blood:
13	chr10:5726410..5728417-chr10:5738015..5741917,3	MCF-7	breast:
14	chr10:5724274..5728540-chr10:5734829..5741563,8	MCF-7	breast:
15	chr10:5725503..5729426-chr10:5853777..5860412,5	MCF-7	breast:
16	chr10:5725427..5729550-chr10:5853446..5856157,4	MCF-7	breast:
17	chr10:5726920..5728949-chr10:5933520..5936437,2	K562	blood:
18	chr10:5726775..5729176-chr10:5734287..5736106,2	MCF-7	breast:
19	chr10:5696053..5698803-chr10:5727232..5729360,2	K562	blood:
20	chr10:5704788..5710194-chr10:5724908..5728833,8	K562	blood:
21	chr10:5725094..5729377-chr10:5927689..5933777,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196372	Chromatin interaction
ENSG00000057608	Chromatin interaction
ENSG00000226647	Chromatin interaction
ENSG00000173848	Chromatin interaction
ENSG00000134461	Chromatin interaction
ENSG00000153560	Chromatin interaction
ENSG00000134452	Chromatin interaction
ENSG00000272764	Chromatin interaction
ENSG00000240577	Chromatin interaction
ENSG00000108021	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11254266	0.90[CHB][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs1578743	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs4748307	0.86[ASN][1000 genomes]
rs4750553	0.85[CHB][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs55913768	0.86[ASN][1000 genomes]
rs56844317	0.82[ASN][1000 genomes]
rs61832743	0.85[ASN][1000 genomes]
rs61832744	0.86[ASN][1000 genomes]
rs72774056	0.86[ASN][1000 genomes]
rs7910414	0.86[ASN][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	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	esv2759729	chr10:5557024-5804780	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv2758209	chr10:5637111-5804780	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv549895	chr10:5712310-5735648	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv1796213	chr10:5716555-5766165	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv522415	chr10:5721653-5768493	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2282457	GDI2	cis	parietal	SCAN
rs2282457	GDI2	Cis_1M	lymphoblastoid	RTeQTL
rs2282457	GDI2	cis	cerebellum	SCAN
rs2282457	IL2RA	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5726000-5727600	Active TSS	Brain Cingulate Gyrus	brain
2	chr10:5726000-5727800	Active TSS	Brain Hippocampus Middle	brain
3	chr10:5726000-5727800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr10:5726000-5727800	Active TSS	Brain Substantia Nigra	brain
5	chr10:5726000-5728000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr10:5726000-5728000	Active TSS	Brain Angular Gyrus	brain
7	chr10:5726000-5728000	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr10:5726000-5728600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr10:5726000-5728800	Active TSS	A549	lung
10	chr10:5726200-5727600	Active TSS	Primary T cells fromperipheralblood	blood
11	chr10:5726200-5727800	Active TSS	Fetal Brain Female	brain
12	chr10:5726200-5728000	Active TSS	Placenta Amnion	Placenta Amnion
13	chr10:5726200-5728200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:5726200-5728200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr10:5726200-5728200	Active TSS	Aorta	Aorta
16	chr10:5726200-5728200	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr10:5726200-5728200	Active TSS	Esophagus	oesophagus
18	chr10:5726200-5728200	Active TSS	Fetal Muscle Trunk	muscle
19	chr10:5726200-5728200	Active TSS	Gastric	stomach
20	chr10:5726200-5728200	Active TSS	Left Ventricle	heart
21	chr10:5726200-5728200	Active TSS	Ovary	ovary
22	chr10:5726200-5728400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr10:5726200-5728400	Active TSS	Colonic Mucosa	Colon
24	chr10:5726200-5728400	Active TSS	Stomach Smooth Muscle	stomach
25	chr10:5726200-5728400	Active TSS	HSMM	muscle
26	chr10:5726200-5728600	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr10:5726200-5728600	Active TSS	Psoas Muscle	Psoas
28	chr10:5726200-5728600	Active TSS	Right Atrium	heart
29	chr10:5726200-5728800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr10:5726400-5727400	Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr10:5726400-5727400	Active TSS	Rectal Smooth Muscle	rectum
32	chr10:5726400-5727600	Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr10:5726400-5727600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr10:5726400-5727600	Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr10:5726400-5727600	Active TSS	Small Intestine	intestine
36	chr10:5726400-5727800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr10:5726400-5727800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr10:5726400-5727800	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr10:5726400-5727800	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr10:5726400-5727800	Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr10:5726400-5727800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr10:5726400-5727800	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr10:5726400-5727800	Active TSS	Brain Anterior Caudate	brain
44	chr10:5726400-5727800	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr10:5726400-5727800	Active TSS	Duodenum Mucosa	Duodenum
46	chr10:5726400-5727800	Active TSS	Fetal Lung	lung
47	chr10:5726400-5727800	Active TSS	Fetal Stomach	stomach
48	chr10:5726400-5727800	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr10:5726400-5728000	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr10:5726400-5728000	Active TSS	iPS-20b Cell Line	embryonic stem cell

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