Variant report

Variant	rs502363
Chromosome Location	chr11:65775592-65775593
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65772806-65775648	U87	brain:	n/a	n/a
2	POLR2A	chr11:65772838-65775713	GM12891	blood:	n/a	n/a
3	CBX3	chr11:65775575-65775977	K562	blood:	n/a	n/a
4	POLR2A	chr11:65775576-65775881	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr11:65774626-65775816	GM12891	blood:	n/a	n/a
6	MAX	chr11:65775519-65776483	ECC-1	luminal epithelium:	n/a	chr11:65775875-65775884
7	POLR2A	chr11:65773416-65776059	GM12878	blood:	n/a	n/a
8	POLR2A	chr11:65775148-65775625	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr11:65773380-65775738	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr11:65772803-65776533	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr11:65772751-65775688	GM12892	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr11:65769812..65778104-chr11:65786537..65794453,15	K562	blood:
2	chr1:152007812..152009419-chr11:65774056..65776325,2	MCF-7	breast:
3	chr11:65764589..65766874-chr11:65774811..65776588,2	K562	blood:
4	chr11:65728544..65730713-chr11:65775327..65777524,2	K562	blood:
5	chr11:65682118..65684018-chr11:65775122..65778045,2	MCF-7	breast:
6	chr11:65730326..65732410-chr11:65773010..65775990,2	MCF-7	breast:
7	chr11:65774068..65777028-chr11:65792820..65794659,2	MCF-7	breast:
8	chr11:65775333..65777143-chr11:65814393..65815931,2	K562	blood:
9	chr11:65773321..65775670-chr11:65834388..65836189,2	K562	blood:
10	chr11:65774540..65776396-chr11:65801301..65804263,2	MCF-7	breast:

No data

Variant related genes	Relation type
CST6	TF binding region
ENSG00000175467	Chromatin interaction
ENSG00000175294	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11227377	0.84[AMR][1000 genomes]
rs1151510	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1151511	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1151514	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1191716	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1192184	0.99[EUR][1000 genomes]
rs1204011	1.00[EUR][1000 genomes]
rs1786172	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1786174	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs506873	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs507672	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs522553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs534201	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540584	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs543952	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs548435	0.83[EUR][1000 genomes]
rs548495	0.98[EUR][1000 genomes]
rs549334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559161	0.82[AMR][1000 genomes]
rs586921	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs590531	1.00[EUR][1000 genomes]
rs610497	0.89[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs615646	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616073	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs619701	1.00[EUR][1000 genomes]
rs622779	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];1.00[EUR][1000 genomes]
rs632640	0.83[EUR][1000 genomes]
rs645571	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs668210	0.85[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs677350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs684546	0.85[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7933510	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
2	nsv832191	chr11:65632329-65806120	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs502363	DKFZp761E198	cis	cerebellum	SCAN
rs502363	SNORD26	cis	parietal	SCAN
rs502363	SNX32	cis	parietal	SCAN
rs502363	PACS1	cis	cerebellum	SCAN
rs502363	RAD9A	cis	cerebellum	SCAN
rs502363	MRPL11	cis	cerebellum	SCAN
rs502363	PCNXL3	cis	cerebellum	SCAN
rs502363	SCGB1D1	cis	cerebellum	SCAN
rs502363	RTN3	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65771000-65776000	Weak transcription	Small Intestine	intestine
2	chr11:65771000-65779000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr11:65771000-65779000	Weak transcription	Aorta	Aorta
4	chr11:65771200-65779000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr11:65771200-65779200	Weak transcription	Right Atrium	heart
6	chr11:65772000-65776200	Weak transcription	Esophagus	oesophagus
7	chr11:65772000-65776600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr11:65772200-65775800	Weak transcription	Colonic Mucosa	Colon
9	chr11:65772200-65776200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr11:65772200-65776400	Weak transcription	Brain Angular Gyrus	brain
11	chr11:65772200-65778800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr11:65772200-65779200	Weak transcription	Gastric	stomach
13	chr11:65772200-65779400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr11:65772200-65779400	Weak transcription	Psoas Muscle	Psoas
15	chr11:65772400-65778200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr11:65772600-65775800	Weak transcription	Fetal Intestine Large	intestine
17	chr11:65772600-65775800	Weak transcription	GM12878-XiMat	blood
18	chr11:65772600-65777200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr11:65772600-65778400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr11:65772800-65775800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr11:65772800-65779200	Weak transcription	Right Ventricle	heart
22	chr11:65773000-65776800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr11:65773200-65775600	Weak transcription	Spleen	Spleen
24	chr11:65773200-65775800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:65773200-65776400	Weak transcription	Brain Substantia Nigra	brain
26	chr11:65773200-65776600	Weak transcription	Left Ventricle	heart
27	chr11:65773200-65776800	Weak transcription	NHDF-Ad	bronchial
28	chr11:65773200-65778000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr11:65773200-65778200	Weak transcription	NH-A	brain
30	chr11:65773200-65779000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr11:65773200-65779200	Weak transcription	Colon Smooth Muscle	Colon
32	chr11:65773400-65776000	Weak transcription	HSMMtube	muscle
33	chr11:65773400-65777600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr11:65773400-65778800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr11:65773400-65779000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr11:65773400-65779000	Weak transcription	Brain Hippocampus Middle	brain
37	chr11:65773400-65779000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr11:65773400-65779000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr11:65773400-65779400	Weak transcription	Ovary	ovary
40	chr11:65773400-65780200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr11:65773600-65775800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:65773600-65776400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr11:65773600-65776400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:65773600-65776600	Weak transcription	Fetal Kidney	kidney
45	chr11:65773600-65777000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr11:65773600-65777000	Weak transcription	Liver	Liver
47	chr11:65773600-65778600	Weak transcription	Brain Anterior Caudate	brain
48	chr11:65773600-65778800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr11:65773600-65778800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr11:65773600-65778800	Weak transcription	Osteobl	bone

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