Variant report

Variant	rs2452682
Chromosome Location	chr11:65812609-65812610
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65812285..65813209-chr11:66025403..66026314,2	MCF-7	breast:
2	chr11:65812475..65816551-chr11:65816982..65820716,11	MCF-7	breast:
3	chr11:65802871..65803569-chr11:65812357..65812898,2	MCF-7	breast:
4	chr11:65792176..65796965-chr11:65812595..65817477,5	MCF-7	breast:
5	chr11:65767772..65771693-chr11:65812597..65815090,3	MCF-7	breast:
6	chr11:65652163..65652746-chr11:65812321..65813006,2	K562	blood:
7	chr11:65788316..65790076-chr11:65810042..65812775,2	K562	blood:
8	chr11:65811021..65815121-chr11:65816503..65821449,7	K562	blood:
9	chr11:65806019..65808419-chr11:65809949..65812700,3	MCF-7	breast:
10	chr11:65810731..65812835-chr11:66047568..66050313,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000087365	Chromatin interaction
ENSG00000175334	Chromatin interaction
ENSG00000174871	Chromatin interaction
ENSG00000175376	Chromatin interaction
ENSG00000174996	Chromatin interaction
ENSG00000175294	Chromatin interaction
ENSG00000238752	Chromatin interaction
ENSG00000175229	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1055615	1.00[CEU][hapmap]
rs10791838	1.00[CEU][hapmap];0.96[GIH][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs10791840	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs10791841	0.89[EUR][1000 genomes]
rs10791845	0.89[GIH][hapmap]
rs10896075	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10896077	1.00[CEU][hapmap]
rs10896081	1.00[CEU][hapmap];0.89[GIH][hapmap]
rs10896089	1.00[CEU][hapmap]
rs10896091	1.00[CEU][hapmap]
rs11227410	1.00[CEU][hapmap]
rs11227411	1.00[CEU][hapmap]
rs11227413	1.00[CEU][hapmap]
rs11227415	1.00[CEU][hapmap];0.89[GIH][hapmap]
rs1125078	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11607393	0.92[CEU][hapmap]
rs12576969	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs12790034	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1783569	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2155201	0.81[CEU][hapmap]
rs2236651	0.81[CEU][hapmap]
rs2236652	0.81[CEU][hapmap]
rs2270448	0.93[GIH][hapmap]
rs2293121	1.00[CEU][hapmap];0.82[GIH][hapmap]
rs2430979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2452681	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs34274349	0.88[EUR][1000 genomes]
rs34450124	0.82[ASN][1000 genomes]
rs3814744	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs3825067	1.00[CEU][hapmap];0.86[GIH][hapmap]
rs3862386	0.93[CEU][hapmap]
rs4261293	0.89[EUR][1000 genomes]
rs4267077	0.85[EUR][1000 genomes]
rs4565902	0.89[EUR][1000 genomes]
rs4614460	0.83[EUR][1000 genomes]
rs476551	0.81[CEU][hapmap]
rs535395	1.00[CEU][hapmap];0.89[GIH][hapmap]
rs61895582	0.91[EUR][1000 genomes]
rs6591199	0.87[EUR][1000 genomes]
rs6591201	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6591202	0.91[EUR][1000 genomes]
rs6591203	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6591207	1.00[CEU][hapmap];0.86[GIH][hapmap]
rs6591208	1.00[CEU][hapmap];0.86[GIH][hapmap]
rs7110838	0.83[EUR][1000 genomes]
rs7120326	1.00[CEU][hapmap];0.89[GIH][hapmap]
rs7120611	0.89[EUR][1000 genomes]
rs730787	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7925123	0.81[CEU][hapmap]
rs7931167	0.91[EUR][1000 genomes]
rs7941469	1.00[CEU][hapmap];0.89[GIH][hapmap]
rs7946917	0.87[CEU][hapmap];0.82[GIH][hapmap]
rs7951770	0.91[EUR][1000 genomes]
rs9326365	0.82[EUR][1000 genomes]
rs9645684	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	nsv897768	chr11:65715210-65842064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
3	nsv897769	chr11:65727799-65828625	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
4	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv897770	chr11:65803750-65824472	Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2452682	POLR2G	cis	parietal	SCAN
rs2452682	GSTM1	trans	lymphoblastoid	seeQTL
rs2452682	ROM1	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65790400-65818600	Weak transcription	HSMM	muscle
2	chr11:65805000-65815800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:65809800-65812800	Weak transcription	Brain Hippocampus Middle	brain
4	chr11:65809800-65815800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:65810200-65813000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr11:65810200-65813000	Weak transcription	Right Ventricle	heart
7	chr11:65811600-65814400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr11:65811800-65814200	Weak transcription	Brain Germinal Matrix	brain
9	chr11:65811800-65814600	Weak transcription	Fetal Brain Female	brain
10	chr11:65812000-65812800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr11:65812000-65812800	Flanking Active TSS	Hela-S3	cervix
12	chr11:65812000-65813400	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr11:65812200-65812800	Enhancers	Osteobl	bone
14	chr11:65812200-65813200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr11:65812200-65813200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:65812200-65813200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr11:65812200-65814800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr11:65812400-65812800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr11:65812400-65812800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr11:65812400-65812800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:65812400-65812800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr11:65812400-65812800	Enhancers	Fetal Heart	heart
23	chr11:65812400-65812800	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr11:65812400-65812800	Flanking Active TSS	A549	lung
25	chr11:65812400-65812800	Flanking Active TSS	GM12878-XiMat	blood
26	chr11:65812400-65812800	Flanking Bivalent TSS/Enh	HepG2	liver
27	chr11:65812400-65812800	Flanking Active TSS	K562	blood
28	chr11:65812400-65813000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:65812400-65813000	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr11:65812400-65813000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:65812400-65813000	Enhancers	Primary B cells from peripheral blood	blood
32	chr11:65812400-65813000	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr11:65812400-65813000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr11:65812400-65813000	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr11:65812400-65813000	Enhancers	Liver	Liver
36	chr11:65812400-65813000	Enhancers	Brain Angular Gyrus	brain
37	chr11:65812400-65813000	Enhancers	Brain Anterior Caudate	brain
38	chr11:65812400-65813000	Enhancers	Fetal Muscle Leg	muscle
39	chr11:65812400-65813000	Bivalent Enhancer	Placenta	Placenta
40	chr11:65812400-65813200	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr11:65812400-65813200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr11:65812400-65813200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:65812400-65813200	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr11:65812400-65813200	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr11:65812400-65813200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr11:65812400-65813200	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr11:65812400-65813200	Enhancers	Primary hematopoietic stem cells	blood
48	chr11:65812400-65813200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr11:65812400-65813200	Enhancers	Muscle Satellite Cultured Cells	--
50	chr11:65812400-65813200	Enhancers	Adipose Nuclei	Adipose

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