Variant report

Variant	rs644306
Chromosome Location	chr11:93475442-93475443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr11:93472992-93475442	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:93469329-93475448	MCF10A-Er-Src	breast:	n/a	n/a
3	ATF3	chr11:93475098-93475449	K562	blood:	n/a	n/a
4	CEBPB	chr11:93474908-93475544	A549	lung:	n/a	n/a
5	REST	chr11:93473826-93475482	H1-neurons	neurons:	n/a	n/a
6	CEBPB	chr11:93473951-93475452	HepG2	liver:	n/a	n/a
7	POLR2A	chr11:93473002-93475493	Hela-S3	cervix:	n/a	n/a
8	MYBL2	chr11:93473775-93475498	HepG2	liver:	n/a	n/a
9	CEBPB	chr11:93475051-93475460	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr11:93465505-93475492	MCF10A-Er-Src	breast:	n/a	n/a
11	CEBPB	chr11:93474543-93475460	A549	lung:	n/a	n/a
12	POLR2A	chr11:93460250-93475527	HepG2	liver:	n/a	n/a
13	RUNX3	chr11:93473924-93475461	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:93469231-93475445	PFSK-1	brain:	n/a	n/a
15	CEBPB	chr11:93473453-93475460	K562	blood:	n/a	chr11:93473547-93473558
16	POLR2A	chr11:93472749-93476093	HepG2	liver:	n/a	n/a
17	MAX	chr11:93473613-93475458	HCT-116	colon:	n/a	chr11:93474081-93474091 chr11:93474082-93474091 chr11:93474080-93474093 chr11:93474442-93474452 chr11:93474082-93474091 chr11:93473728-93473737 chr11:93474215-93474223 chr11:93474081-93474092 chr11:93474082-93474091 chr11:93474081-93474092 chr11:93474324-93474333 chr11:93474082-93474092 chr11:93474755-93474764 chr11:93473729-93473738
18	TBP	chr11:93473508-93475449	Hela-S3	cervix:	n/a	n/a
19	PML	chr11:93472967-93475541	GM12878	blood:	n/a	chr11:93473730-93473739
20	POLR2A	chr11:93472326-93475450	GM12892	blood:	n/a	n/a
21	MAX	chr11:93473659-93475495	HepG2	liver:	n/a	chr11:93474081-93474091 chr11:93474082-93474091 chr11:93474080-93474093 chr11:93474442-93474452 chr11:93474082-93474091 chr11:93473728-93473737 chr11:93474215-93474223 chr11:93474081-93474092 chr11:93474082-93474091 chr11:93474081-93474092 chr11:93474324-93474333 chr11:93474082-93474092 chr11:93474755-93474764 chr11:93473729-93473738
22	POLR2A	chr11:93460630-93475546	PFSK-1	brain:	n/a	n/a
23	CEBPB	chr11:93475011-93475461	ECC-1	luminal epithelium:	n/a	n/a
24	HEY1	chr11:93472308-93475444	HepG2	liver:	n/a	n/a
25	MAX	chr11:93473775-93475463	HCT-116	colon:	n/a	chr11:93474081-93474091 chr11:93474082-93474091 chr11:93474080-93474093 chr11:93474442-93474452 chr11:93474082-93474091 chr11:93474215-93474223 chr11:93474081-93474092 chr11:93474082-93474091 chr11:93474081-93474092 chr11:93474324-93474333 chr11:93474082-93474092 chr11:93474755-93474764
26	CEBPB	chr11:93474538-93475466	HepG2	liver:	n/a	n/a
27	POLR2A	chr11:93459823-93475456	HepG2	liver:	n/a	n/a
28	MYBL2	chr11:93473873-93475462	HepG2	liver:	n/a	n/a
29	BRCA1	chr11:93472565-93475496	Hela-S3	cervix:	n/a	chr11:93474702-93474711
30	SP1	chr11:93474481-93475485	HepG2	liver:	n/a	chr11:93474801-93474813 chr11:93474833-93474842 chr11:93474831-93474843 chr11:93474832-93474842 chr11:93474828-93474842 chr11:93474801-93474813 chr11:93474832-93474841
31	POLR2A	chr11:93470174-93475516	PANC-1	pancreas:	n/a	n/a
32	MAX	chr11:93473821-93475522	HepG2	liver:	n/a	chr11:93474081-93474091 chr11:93474082-93474091 chr11:93474080-93474093 chr11:93474442-93474452 chr11:93474082-93474091 chr11:93474215-93474223 chr11:93474081-93474092 chr11:93474082-93474091 chr11:93474081-93474092 chr11:93474324-93474333 chr11:93474082-93474092 chr11:93474755-93474764
33	POLR2A	chr11:93472718-93475483	HL-60	blood:	n/a	n/a
34	MXI1	chr11:93472736-93475540	IMR90	lung:	n/a	chr11:93474081-93474090 chr11:93474081-93474090 chr11:93474083-93474092
35	CEBPB	chr11:93473178-93475480	Hela-S3	cervix:	n/a	chr11:93473547-93473558
36	GTF3C2	chr11:93474912-93475445	Hela-S3	cervix:	n/a	n/a
37	HCFC1	chr11:93470846-93475552	Hela-S3	cervix:	n/a	n/a
38	EP300	chr11:93474601-93475466	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr11:93470925-93475512	HepG2	liver:	n/a	n/a
40	NFIC	chr11:93474343-93475480	HepG2	liver:	n/a	n/a
41	CEBPD	chr11:93475003-93475446	HepG2	liver:	n/a	n/a
42	ZNF384	chr11:93473476-93475456	K562	blood:	n/a	n/a
43	HEY1	chr11:93473864-93475532	HepG2	liver:	n/a	n/a
44	POLR2A	chr11:93472961-93475514	GM12878	blood:	n/a	n/a
45	MXI1	chr11:93473168-93475449	Hela-S3	cervix:	n/a	chr11:93474081-93474090 chr11:93474081-93474090 chr11:93474083-93474092
46	TEAD4	chr11:93474342-93475509	HepG2	liver:	n/a	n/a
47	MBD4	chr11:93473810-93475443	HepG2	liver:	n/a	n/a
48	POLR2A	chr11:93471010-93475524	GM12878	blood:	n/a	n/a
49	MAX	chr11:93473172-93475455	Hela-S3	cervix:	n/a	chr11:93474081-93474091 chr11:93474082-93474091 chr11:93474080-93474093 chr11:93474442-93474452 chr11:93474082-93474091 chr11:93473728-93473737 chr11:93474215-93474223 chr11:93474081-93474092 chr11:93474082-93474091 chr11:93474081-93474092 chr11:93474324-93474333 chr11:93474082-93474092 chr11:93474755-93474764 chr11:93473729-93473738
50	NR2F2	chr11:93473565-93475472	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:93472800..93476056-chr11:93515203..93522725,16	MCF-7	breast:
2	chr11:93475425..93477478-chr11:93478372..93480082,2	MCF-7	breast:
3	chr11:93473689..93475609-chr11:94224502..94227416,2	K562	blood:
4	chr11:93393391..93395168-chr11:93473052..93476024,2	K562	blood:
5	chr11:93475114..93477251-chr11:93501701..93505536,3	K562	blood:
6	chr11:93472589..93476859-chr11:93528988..93534877,8	K562	blood:
7	chr11:93462890..93477443-chr11:93512595..93526939,73	K562	blood:
8	chr11:93473309..93475727-chr11:93520593..93523450,3	MCF-7	breast:
9	chr11:93393652..93395603-chr11:93473209..93475607,2	MCF-7	breast:
10	chr11:93468490..93476714-chr11:93515963..93520210,25	MCF-7	breast:
11	chr11:93473294..93475669-chr11:94705977..94707605,2	MCF-7	breast:
12	chr11:93475019..93477218-chr11:93528354..93530806,2	K562	blood:
13	chr11:93472363..93476142-chr11:93531511..93536193,5	K562	blood:
14	chr11:93475427..93477078-chr11:93480358..93482753,2	MCF-7	breast:
15	chr11:93468648..93476533-chr11:93513626..93520226,41	K562	blood:

Variant related genes	Relation type
TAF1D	TF binding region
C11orf54	TF binding region
ENSG00000186280	Chromatin interaction
ENSG00000020922	Chromatin interaction
ENSG00000182919	Chromatin interaction
ENSG00000238437	Chromatin interaction
ENSG00000150316	Chromatin interaction
ENSG00000265292	Chromatin interaction
ENSG00000166004	Chromatin interaction
ENSG00000168876	Chromatin interaction
ENSG00000042429	Chromatin interaction
ENSG00000166012	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10831103	0.81[ASN][1000 genomes]
rs10831104	1.00[JPT][hapmap]
rs11603364	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17650369	0.87[CHD][hapmap];0.87[YRI][hapmap]
rs3097323	0.92[GIH][hapmap]
rs607349	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.88[ASN][1000 genomes]
rs613610	0.88[ASN][1000 genomes]
rs643261	1.00[CHB][hapmap]
rs685865	0.81[ASN][1000 genomes]
rs7310	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv898182	chr11:93381845-93637462	Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS 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	108 gene(s)	inside rSNPs	diseases
3	nsv832232	chr11:93401314-93549438	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs644306	GPR83	cis	cerebellum	SCAN
rs644306	FUT4	cis	cerebellum	SCAN
rs644306	C11orf54	cis	parietal	SCAN
rs644306	SCARNA9	cis	cerebellum	SCAN
rs644306	SCARNA9	cis	parietal	SCAN
rs644306	C11orf54	cis	cerebellum	SCAN
rs644306	MED17	cis	cerebellum	SCAN
rs644306	ENDOD1	cis	cerebellum	SCAN
rs644306	MED17	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93470800-93475800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:93472000-93475800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:93472200-93475600	Active TSS	Ovary	ovary
4	chr11:93472200-93475800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:93472200-93475800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr11:93472200-93475800	Active TSS	Fetal Intestine Small	intestine
7	chr11:93472600-93475600	Active TSS	Duodenum Mucosa	Duodenum
8	chr11:93472600-93475800	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr11:93472600-93475800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:93472600-93475800	Active TSS	GM12878-XiMat	blood
11	chr11:93472600-93476000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:93472800-93475800	Active TSS	NH-A	brain
13	chr11:93472800-93476000	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr11:93473000-93475600	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr11:93473000-93475600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:93473000-93475600	Active TSS	HMEC	breast
17	chr11:93473000-93475800	Active TSS	Hela-S3	cervix
18	chr11:93473000-93476000	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr11:93473000-93476200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr11:93473000-93476200	Active TSS	Fetal Kidney	kidney
21	chr11:93473200-93475600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr11:93473200-93475600	Active TSS	HUVEC	blood vessel
23	chr11:93473400-93475600	Active TSS	Brain Angular Gyrus	brain
24	chr11:93473400-93475600	Active TSS	Fetal Intestine Large	intestine
25	chr11:93473400-93475600	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr11:93473400-93475600	Active TSS	NHDF-Ad	bronchial
27	chr11:93473400-93475800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr11:93473400-93475800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr11:93473400-93475800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr11:93473400-93475800	Active TSS	Aorta	Aorta
31	chr11:93473400-93475800	Active TSS	Liver	Liver
32	chr11:93473400-93475800	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr11:93473400-93475800	Active TSS	Right Ventricle	heart
34	chr11:93473400-93475800	Active TSS	Small Intestine	intestine
35	chr11:93473400-93475800	Active TSS	HSMMtube	muscle
36	chr11:93473400-93475800	Active TSS	NHEK	skin
37	chr11:93473400-93476000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr11:93473400-93476000	Active TSS	Fetal Brain Female	brain
39	chr11:93473600-93475600	Active TSS	H1 Cell Line	embryonic stem cell
40	chr11:93473600-93475600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr11:93473600-93475600	Active TSS	Brain Anterior Caudate	brain
42	chr11:93473600-93475600	Active TSS	Brain Hippocampus Middle	brain
43	chr11:93473600-93475600	Active TSS	Fetal Lung	lung
44	chr11:93473600-93475600	Active TSS	Placenta	Placenta
45	chr11:93473600-93475600	Active TSS	Fetal Stomach	stomach
46	chr11:93473600-93475600	Active TSS	Left Ventricle	heart
47	chr11:93473600-93475600	Active TSS	Stomach Smooth Muscle	stomach
48	chr11:93473600-93475800	Active TSS	Brain Germinal Matrix	brain
49	chr11:93473600-93475800	Active TSS	Pancreas	Pancrea
50	chr11:93473600-93475800	Active TSS	Psoas Muscle	Psoas

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