Variant report

Variant	rs668546
Chromosome Location	chr11:93478005-93478006
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CUX1	chr11:93477966-93478355	K562	blood:	n/a	n/a
2	POLR2A	chr11:93477859-93478772	HepG2	liver:	n/a	n/a
3	CUX1	chr11:93477890-93478056	GM12878	blood:	n/a	n/a
4	HEY1	chr11:93477758-93478910	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:93477996-93478367	GM12878	blood:	n/a	n/a
6	NR3C1	chr11:93478000-93478467	A549	lung:	n/a	n/a
7	MYBL2	chr11:93477782-93478822	HepG2	liver:	n/a	n/a
8	POLR2A	chr11:93477910-93478127	K562	blood:	n/a	n/a
9	TEAD4	chr11:93477906-93478935	HepG2	liver:	n/a	n/a
10	EBF1	chr11:93477822-93478610	GM12878	blood:	n/a	n/a
11	POLR2A	chr11:93477849-93478819	HepG2	liver:	n/a	n/a
12	FOXA1	chr11:93477807-93478230	HepG2	liver:	n/a	n/a
13	MBD4	chr11:93477730-93478788	HepG2	liver:	n/a	n/a
14	POLR2A	chr11:93477916-93478143	HepG2	liver:	n/a	n/a
15	NR3C1	chr11:93477906-93478704	A549	lung:	n/a	n/a
16	MYBL2	chr11:93477735-93479056	HepG2	liver:	n/a	n/a
17	POLR2A	chr11:93477779-93478915	HepG2	liver:	n/a	n/a
18	POLR2A	chr11:93476771-93478601	K562	blood:	n/a	n/a
19	POLR2A	chr11:93477884-93478557	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr11:93477885-93478467	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr11:93477968-93478850	HepG2	liver:	n/a	n/a
22	HEY1	chr11:93477870-93478911	HepG2	liver:	n/a	n/a
23	POLR2A	chr11:93477925-93478045	A549	lung:	n/a	n/a
24	NR3C1	chr11:93477821-93478767	A549	lung:	n/a	n/a
25	NR3C1	chr11:93477850-93478750	A549	lung:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:93476858..93478518-chr11:93487193..93489056,2	K562	blood:
2	chr11:93477638..93479827-chr11:93520843..93522427,2	K562	blood:
3	chr11:93472413..93474850-chr11:93477709..93480682,4	MCF-7	breast:
4	chr11:93476133..93478547-chr11:93497585..93500296,2	K562	blood:

No data

Variant related genes	Relation type
C11orf54	TF binding region
TAF1D	TF binding region
ENSG00000182919	Chromatin interaction
ENSG00000042429	Chromatin interaction
ENSG00000166012	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10831103	0.83[EUR][1000 genomes]
rs11020511	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11603339	0.83[EUR][1000 genomes]
rs11603364	0.83[EUR][1000 genomes]
rs2895508	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs596052	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs607349	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs613610	0.87[EUR][1000 genomes]
rs621801	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs635963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs643261	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs677867	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs685865	0.85[EUR][1000 genomes]
rs7310	0.87[AMR][1000 genomes];0.96[EUR][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs668546	C11orf54	cis	Esophagus Mucosa	GTEx
rs668546	C11orf54	cis	Skin Sun Exposed Lower leg	GTEx
rs668546	MED17	Cis_1M	lymphoblastoid	RTeQTL
rs668546	C11orf54	cis	Artery Tibial	GTEx
rs668546	C11orf54	cis	lung	GTEx
rs668546	C11orf54	cis	Esophagus Muscularis	GTEx
rs668546	C11orf54	cis	Artery Aorta	GTEx
rs668546	C11orf54	cis	Muscle Skeletal	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93475200-93497000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:93475400-93478200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:93475400-93478600	Enhancers	Stomach Mucosa	stomach
4	chr11:93475400-93490800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:93475400-93490800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:93475600-93490000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr11:93475600-93497000	Weak transcription	NHDF-Ad	bronchial
8	chr11:93475800-93478200	Enhancers	Fetal Heart	heart
9	chr11:93475800-93488400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr11:93475800-93488400	Weak transcription	Aorta	Aorta
11	chr11:93476000-93478200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr11:93476000-93478200	Weak transcription	Brain Substantia Nigra	brain
13	chr11:93476000-93481800	Weak transcription	Thymus	Thymus
14	chr11:93476000-93483000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr11:93476000-93486600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr11:93476000-93486800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr11:93476000-93488400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr11:93476000-93488400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr11:93476000-93488400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr11:93476000-93488400	Weak transcription	HSMMtube	muscle
21	chr11:93476000-93490600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr11:93476000-93491400	Weak transcription	Osteobl	bone
23	chr11:93476000-93495600	Weak transcription	HUVEC	blood vessel
24	chr11:93476000-93497000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr11:93476000-93497200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr11:93476000-93498800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr11:93476200-93478200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:93476200-93478400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr11:93476200-93482400	Weak transcription	Primary T cells from cord blood	blood
30	chr11:93476200-93483800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr11:93476200-93486800	Weak transcription	Colon Smooth Muscle	Colon
32	chr11:93476200-93488000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr11:93476200-93499800	Weak transcription	NH-A	brain
34	chr11:93476400-93481800	Weak transcription	Primary B cells from cord blood	blood
35	chr11:93476600-93478600	Enhancers	Right Atrium	heart
36	chr11:93476600-93486400	Weak transcription	GM12878-XiMat	blood
37	chr11:93476600-93487200	Weak transcription	Fetal Brain Male	brain
38	chr11:93476600-93488400	Weak transcription	Colonic Mucosa	Colon
39	chr11:93476800-93486800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr11:93477000-93486600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr11:93477000-93487000	Weak transcription	Hela-S3	cervix
42	chr11:93477000-93488400	Weak transcription	Esophagus	oesophagus
43	chr11:93477000-93491200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr11:93477200-93478200	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr11:93477200-93478200	Weak transcription	Fetal Brain Female	brain
46	chr11:93477200-93478200	Enhancers	Fetal Intestine Large	intestine
47	chr11:93477200-93478200	Weak transcription	Lung	lung
48	chr11:93477200-93478200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr11:93477200-93478400	Enhancers	Fetal Lung	lung
50	chr11:93477200-93478600	Enhancers	Rectal Mucosa Donor 31	rectum

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