Variant report

Variant	rs2282498
Chromosome Location	chr11:64855986-64855987
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:64855909-64857655	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:64854584-64856843	K562	blood:	n/a	n/a
3	POLR2A	chr11:64855899-64857664	GM12892	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64540271..64542965-chr11:64854010..64856137,2	MCF-7	breast:
2	chr11:64849716..64856389-chr11:64935136..64940419,9	K562	blood:
3	chr11:64691650..64693175-chr11:64855147..64856721,2	K562	blood:
4	chr11:64804480..64810811-chr11:64850224..64856247,12	K562	blood:
5	chr11:64644835..64647462-chr11:64855986..64857500,2	MCF-7	breast:
6	chr11:64813509..64815551-chr11:64854732..64857551,2	K562	blood:
7	chr11:64793383..64797474-chr11:64849331..64856424,6	K562	blood:

No data

Variant related genes	Relation type
VPS51	TF binding region
CDCA5	TF binding region
ENSG00000168060	Chromatin interaction
ENSG00000270775	Chromatin interaction
ENSG00000168061	Chromatin interaction
ENSG00000068971	Chromatin interaction
ENSG00000204710	Chromatin interaction
ENSG00000110047	Chromatin interaction
ENSG00000110025	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11227118	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231929	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs1129195	0.97[GIH][hapmap];0.87[TSI][hapmap]
rs1196048	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2282499	0.97[GIH][hapmap];0.89[TSI][hapmap]
rs2507814	0.83[JPT][hapmap]
rs36057475	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782094	0.92[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3802936	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3825073	0.86[CHB][hapmap]
rs3862374	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs477539	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs484182	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs486984	0.82[JPT][hapmap]
rs489489	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs496427	0.96[ASN][1000 genomes]
rs498636	0.83[ASN][1000 genomes]
rs502333	0.84[JPT][hapmap]
rs534236	0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs548150	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs564966	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[ASN][1000 genomes]
rs566908	1.00[YRI][hapmap]
rs653111	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6591869	0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs7123226	0.84[EUR][1000 genomes]
rs7130183	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7943007	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs947799	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9971546	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv897709	chr11:64772545-64870779	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv897710	chr11:64772545-64885445	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv897711	chr11:64772545-64900270	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2282498	SCGB2A2	cis	cerebellum	SCAN
rs2282498	SNORD31	cis	parietal	SCAN
rs2282498	SUV420H1	cis	parietal	SCAN
rs2282498	SNX15	cis	parietal	SCAN
rs2282498	SNORD22	cis	parietal	SCAN
rs2282498	RAB1B	cis	parietal	SCAN
rs2282498	ZNHIT2	cis	cerebellum	SCAN
rs2282498	FADS1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64852400-64863600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:64852600-64863200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:64852600-64863600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:64852800-64856800	Strong transcription	Left Ventricle	heart
5	chr11:64852800-64856800	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:64852800-64857000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr11:64852800-64857200	Strong transcription	Right Ventricle	heart
8	chr11:64852800-64857400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr11:64852800-64857400	Strong transcription	Ovary	ovary
10	chr11:64852800-64857600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:64852800-64857600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:64852800-64857800	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr11:64852800-64858200	Strong transcription	Fetal Muscle Trunk	muscle
14	chr11:64852800-64858400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:64852800-64858400	Strong transcription	Lung	lung
16	chr11:64852800-64863200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr11:64852800-64863400	Weak transcription	Psoas Muscle	Psoas
18	chr11:64853000-64856000	Weak transcription	Stomach Mucosa	stomach
19	chr11:64853000-64856800	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr11:64853000-64856800	Strong transcription	Fetal Brain Female	brain
21	chr11:64853000-64857200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr11:64853000-64857400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:64853000-64857600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr11:64853000-64857600	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr11:64853000-64858000	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr11:64853000-64858400	Strong transcription	Fetal Stomach	stomach
27	chr11:64853200-64856400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:64853200-64856800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr11:64853200-64856800	Strong transcription	Fetal Lung	lung
30	chr11:64853200-64856800	Strong transcription	NHEK	skin
31	chr11:64853200-64857000	Strong transcription	Primary B cells from cord blood	blood
32	chr11:64853200-64857000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr11:64853200-64857200	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr11:64853200-64857200	Strong transcription	Colonic Mucosa	Colon
35	chr11:64853200-64857200	Strong transcription	Rectal Smooth Muscle	rectum
36	chr11:64853200-64857400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr11:64853200-64857400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr11:64853200-64857400	Strong transcription	Brain Cingulate Gyrus	brain
39	chr11:64853200-64857400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr11:64853200-64857400	Strong transcription	Duodenum Mucosa	Duodenum
41	chr11:64853200-64857400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr11:64853200-64857400	Strong transcription	Gastric	stomach
43	chr11:64853200-64857400	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr11:64853200-64857600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:64853200-64857600	Strong transcription	Brain Germinal Matrix	brain
46	chr11:64853200-64857800	Strong transcription	Adipose Nuclei	Adipose
47	chr11:64853200-64858200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr11:64853200-64858400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:64853200-64858400	Strong transcription	Fetal Muscle Leg	muscle
50	chr11:64853200-64858400	Strong transcription	Placenta	Placenta

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