Variant report

Variant	rs55853079
Chromosome Location	chr11:66277969-66277970
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	POLR2A	chr11:66277828-66278394	U87	brain:	n/a	n/a
2	BCLAF1	chr11:66277817-66278327	GM12878	blood:	n/a	n/a
3	TAF1	chr11:66277841-66278262	Hela-S3	cervix:	n/a	n/a
4	SETDB1	chr11:66277862-66278306	U2OS	brain:	n/a	n/a
5	TAF7	chr11:66277830-66278392	H1-hESC	embryonic stem cell:	n/a	n/a
6	THAP1	chr11:66277965-66278289	K562	blood:	n/a	n/a
7	POLR2A	chr11:66277899-66278354	GM12891	blood:	n/a	n/a
8	HMGN3	chr11:66277936-66278294	K562	blood:	n/a	n/a
9	POLR2A	chr11:66277811-66278380	GM12891	blood:	n/a	n/a
10	KAP1	chr11:66277836-66278293	U2OS	brain:	n/a	n/a
11	FOXP2	chr11:66277864-66278285	SK-N-MC	brain:	n/a	n/a
12	MAX	chr11:66277883-66278487	NB4	blood:	n/a	chr11:66278094-66278104
13	RCOR1	chr11:66277905-66278360	HepG2	liver:	n/a	n/a
14	FOXP2	chr11:66277965-66278211	PFSK-1	brain:	n/a	n/a
15	GABPA	chr11:66277796-66278239	K562	blood:	n/a	n/a
16	POLR2A	chr11:66277838-66278462	GM12878	blood:	n/a	n/a
17	EP300	chr11:66277953-66278153	SK-N-SH_RA	brain:	n/a	n/a
18	SP1	chr11:66277743-66278291	H1-hESC	embryonic stem cell:	n/a	chr11:66278093-66278105 chr11:66278094-66278103 chr11:66278095-66278104 chr11:66278094-66278104 chr11:66278093-66278105 chr11:66278058-66278071
19	ELF1	chr11:66277839-66278243	A549	lung:	n/a	n/a
20	BCLAF1	chr11:66277759-66278258	K562	blood:	n/a	n/a
21	SIX5	chr11:66277922-66278211	K562	blood:	n/a	n/a
22	YY1	chr11:66277920-66278335	NT2-D1	testis:	n/a	chr11:66278126-66278138
23	TAF7	chr11:66277793-66278257	H1-hESC	embryonic stem cell:	n/a	n/a
24	TEAD4	chr11:66277743-66278495	K562	blood:	n/a	n/a
25	TAF1	chr11:66277936-66278288	HepG2	liver:	n/a	n/a
26	YY1	chr11:66277830-66278487	H1-hESC	embryonic stem cell:	n/a	chr11:66278126-66278138
27	POLR2A	chr11:66277794-66278337	HCT-116	colon:	n/a	n/a
28	CEBPB	chr11:66277785-66278330	GM12878	blood:	n/a	n/a
29	EP300	chr11:66277909-66278210	HepG2	liver:	n/a	n/a
30	HCFC1	chr11:66277826-66278356	K562	blood:	n/a	n/a
31	CTCF	chr11:66277860-66278010	MCF-7	breast:	n/a	n/a
32	UBTF	chr11:66277859-66278204	K562	blood:	n/a	n/a
33	REST	chr11:66277706-66278464	A549	lung:	n/a	n/a
34	CREB1	chr11:66277775-66278474	HepG2	liver:	n/a	n/a
35	BHLHE40	chr11:66277884-66278303	K562	blood:	n/a	n/a
36	GABPA	chr11:66277814-66278307	Hela-S3	cervix:	n/a	n/a
37	SP1	chr11:66277836-66278308	GM12878	blood:	n/a	chr11:66278093-66278105 chr11:66278094-66278103 chr11:66278095-66278104 chr11:66278094-66278104 chr11:66278093-66278105 chr11:66278058-66278071
38	PBX3	chr11:66277792-66278365	SK-N-SH	brain:	n/a	n/a
39	MXI1	chr11:66277874-66278854	IMR90	lung:	n/a	chr11:66278105-66278120 chr11:66278107-66278122
40	ELK1	chr11:66277899-66278252	K562	blood:	n/a	n/a
41	BHLHE40	chr11:66277890-66278524	GM12878	blood:	n/a	n/a
42	YY1	chr11:66277922-66278381	A549	lung:	n/a	chr11:66278126-66278138
43	YY1	chr11:66277826-66278424	K562	blood:	n/a	chr11:66278126-66278138
44	STAT1	chr11:66277863-66278246	GM12878	blood:	n/a	n/a
45	CTCF	chr11:66277820-66277970	HPF	lung:	n/a	n/a
46	CHD2	chr11:66277910-66278255	H1-hESC	embryonic stem cell:	n/a	n/a
47	CHD2	chr11:66277936-66278352	GM12878	blood:	n/a	n/a
48	SRF	chr11:66277712-66278420	MCF-7	breast:	n/a	chr11:66278094-66278104
49	TAF1	chr11:66277831-66278348	GM12892	blood:	n/a	n/a
50	YY1	chr11:66277828-66278646	GM12892	blood:	n/a	chr11:66278126-66278138

No.	Distal block	Cell Line	Cell type
1	chr11:66240065..66243058-chr11:66275897..66279906,3	MCF-7	breast:
2	chr11:66277230..66279524-chr11:66443471..66447477,3	K562	blood:
3	chr11:66276194..66279522-chr11:66281470..66284393,4	MCF-7	breast:
4	chr11:66271226..66274092-chr11:66277706..66279394,2	K562	blood:
5	chr11:66277351..66279482-chr11:66383310..66385762,3	K562	blood:
6	chr11:66275530..66280458-chr11:66280685..66284919,6	K562	blood:
7	chr11:66244850..66249884-chr11:66274125..66278778,6	MCF-7	breast:
8	chr11:66277334..66280308-chr11:66282116..66284343,2	MCF-7	breast:
9	chr11:66277255..66279154-chr11:66443896..66445716,2	MCF-7	breast:
10	chr11:66277249..66279573-chr11:66442892..66445928,3	K562	blood:
11	chr11:66234037..66235984-chr11:66277120..66279562,2	MCF-7	breast:

Variant related genes	Relation type
BBS1	TF binding region
ENSG00000174547	Chromatin interaction
ENSG00000174483	Chromatin interaction
ENSG00000248643	Chromatin interaction
ENSG00000174516	Chromatin interaction
ENSG00000255517	Chromatin interaction
ENSG00000173914	Chromatin interaction
ENSG00000254986	Chromatin interaction
ENSG00000239306	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10896126	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11110	0.85[EUR][1000 genomes]
rs11227485	0.85[EUR][1000 genomes]
rs12793712	0.82[EUR][1000 genomes]
rs2282640	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7951189	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]

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	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
2	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv832193	chr11:66120339-66278805	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv468601	chr11:66234023-66296114	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv555224	chr11:66234023-66296114	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers 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 miRNA target site	94 gene(s)	inside rSNPs	diseases
7	nsv934228	chr11:66277759-66288927	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55853079	CTSF	cis	Esophagus Muscularis	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66248600-66278000	Weak transcription	NHDF-Ad	bronchial
2	chr11:66261200-66278000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:66264600-66278000	Weak transcription	HMEC	breast
4	chr11:66266600-66278000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:66272800-66278000	Weak transcription	Lung	lung
6	chr11:66272800-66278000	Weak transcription	NHLF	lung
7	chr11:66273000-66278000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:66273200-66278000	Weak transcription	Gastric	stomach
9	chr11:66277200-66278000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr11:66277200-66278000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr11:66277200-66278000	Enhancers	Spleen	Spleen
12	chr11:66277400-66278000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:66277600-66278000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:66277600-66278000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr11:66277600-66278000	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr11:66277600-66278000	Flanking Active TSS	Colon Smooth Muscle	Colon
17	chr11:66277600-66278000	Enhancers	Fetal Brain Male	brain
18	chr11:66277600-66278000	Flanking Active TSS	Fetal Lung	lung
19	chr11:66277600-66278000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr11:66277600-66278000	Enhancers	Small Intestine	intestine
21	chr11:66277600-66278000	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr11:66277600-66278000	Flanking Active TSS	HepG2	liver
23	chr11:66277600-66278000	Flanking Active TSS	K562	blood
24	chr11:66277600-66278200	Enhancers	Stomach Mucosa	stomach
25	chr11:66277600-66278200	Flanking Active TSS	Dnd41	blood
26	chr11:66277600-66278400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr11:66277600-66278400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:66277600-66278400	Active TSS	Brain Cingulate Gyrus	brain
29	chr11:66277600-66278400	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr11:66277600-66278400	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr11:66277600-66278400	Active TSS	Ovary	ovary
32	chr11:66277600-66278400	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr11:66277600-66278400	Active TSS	Rectal Smooth Muscle	rectum
34	chr11:66277600-66278400	Active TSS	Hela-S3	cervix
35	chr11:66277600-66278600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:66277600-66278600	Active TSS	Brain Germinal Matrix	brain
37	chr11:66277600-66278600	Active TSS	Right Atrium	heart
38	chr11:66277600-66278800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr11:66277600-66278800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr11:66277600-66278800	Flanking Active TSS	Liver	Liver
41	chr11:66277600-66278800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr11:66277600-66279000	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr11:66277600-66279000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr11:66277600-66279000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr11:66277600-66279200	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr11:66277600-66279200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr11:66277800-66278000	Enhancers	H1 Cell Line	embryonic stem cell
48	chr11:66277800-66278000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:66277800-66278000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr11:66277800-66278000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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