Variant report

Variant	rs7939541
Chromosome Location	chr11:9590389-9590390
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	chr11:9590317-9591033	U87	brain:	n/a	n/a
2	RUNX3	chr11:9590358-9590773	GM12878	blood:	n/a	n/a
3	SIN3AK20	chr11:9590197-9590850	MCF-7	breast:	n/a	n/a
4	RFX5	chr11:9590386-9591111	HepG2	liver:	n/a	chr11:9590549-9590564 chr11:9590552-9590561 chr11:9590547-9590563 chr11:9590550-9590564 chr11:9590548-9590562
5	NR3C1	chr11:9590326-9590833	ECC-1	luminal epithelium:	n/a	chr11:9590650-9590664 chr11:9590649-9590665 chr11:9590499-9590514 chr11:9590649-9590665 chr11:9590650-9590664 chr11:9590649-9590665 chr11:9590646-9590667 chr11:9590649-9590665
6	FOXA1	chr11:9590322-9590746	T-47D	breast:	n/a	n/a
7	E2F4	chr11:9590344-9591001	MCF10A-Er-Src	breast:	n/a	chr11:9590600-9590609
8	POLR2A	chr11:9589813-9591762	IMR90	lung:	n/a	n/a
9	FOXA1	chr11:9590300-9590754	T-47D	breast:	n/a	n/a
10	FOXA1	chr11:9590351-9591206	HepG2	liver:	n/a	n/a
11	EP300	chr11:9590181-9591111	T-47D	breast:	n/a	chr11:9590789-9590803 chr11:9590587-9590601
12	STAT3	chr11:9590135-9591064	MCF10A-Er-Src	breast:	n/a	n/a
13	FOXA1	chr11:9590337-9591187	HepG2	liver:	n/a	n/a
14	POLR2A	chr11:9590349-9591063	SK-N-MC	brain:	n/a	n/a
15	SP1	chr11:9590236-9590623	H1-hESC	embryonic stem cell:	n/a	n/a
16	TEAD4	chr11:9590281-9591140	K562	blood:	n/a	n/a
17	FOS	chr11:9590360-9590825	MCF10A-Er-Src	breast:	n/a	n/a
18	GATA3	chr11:9590030-9591256	MCF-7	breast:	n/a	n/a
19	GATA3	chr11:9590213-9591251	MCF-7	breast:	n/a	n/a
20	REST	chr11:9590377-9591246	A549	lung:	n/a	n/a
21	SP1	chr11:9590160-9590740	H1-hESC	embryonic stem cell:	n/a	n/a
22	BRCA1	chr11:9590335-9590807	Hela-S3	cervix:	n/a	n/a
23	TCF12	chr11:9590215-9591358	A549	lung:	n/a	n/a
24	NR3C1	chr11:9590388-9590782	A549	lung:	n/a	chr11:9590650-9590664 chr11:9590649-9590665 chr11:9590499-9590514 chr11:9590649-9590665 chr11:9590650-9590664 chr11:9590649-9590665 chr11:9590646-9590667 chr11:9590649-9590665
25	FOXA1	chr11:9590341-9591135	HepG2	liver:	n/a	n/a
26	MYC	chr11:9590228-9591162	MCF10A-Er-Src	breast:	n/a	n/a
27	EP300	chr11:9590127-9590847	ECC-1	luminal epithelium:	n/a	chr11:9590789-9590803 chr11:9590587-9590601
28	USF1	chr11:9590345-9591116	A549	lung:	n/a	n/a
29	POLR2A	chr11:9590185-9591094	HepG2	liver:	n/a	n/a
30	RFX5	chr11:9589769-9591208	SK-N-SH	brain:	n/a	chr11:9590549-9590564 chr11:9590552-9590561 chr11:9590547-9590563 chr11:9590550-9590564 chr11:9590548-9590562 chr11:9590381-9590395
31	STAT3	chr11:9590295-9591046	MCF10A-Er-Src	breast:	n/a	n/a
32	FOXA2	chr11:9590345-9590686	HepG2	liver:	n/a	n/a
33	POLR2A	chr11:9590361-9591147	HepG2	liver:	n/a	n/a
34	CEBPB	chr11:9590385-9591147	A549	lung:	n/a	n/a
35	MAX	chr11:9590015-9590860	ECC-1	luminal epithelium:	n/a	n/a
36	CEBPB	chr11:9590314-9591196	MCF-7	breast:	n/a	n/a
37	NR3C1	chr11:9590315-9591246	A549	lung:	n/a	chr11:9590650-9590664 chr11:9590649-9590665 chr11:9590499-9590514 chr11:9590649-9590665 chr11:9590650-9590664 chr11:9590649-9590665 chr11:9590646-9590667 chr11:9590649-9590665
38	EP300	chr11:9590328-9591303	A549	lung:	n/a	chr11:9590789-9590803 chr11:9590587-9590601
39	JUND	chr11:9590098-9591129	T-47D	breast:	n/a	n/a
40	POLR2A	chr11:9590386-9590807	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr11:9590305-9591203	PANC-1	pancreas:	n/a	n/a
42	EP300	chr11:9590353-9590745	H1-hESC	embryonic stem cell:	n/a	chr11:9590587-9590601
43	RFX5	chr11:9590354-9590799	Hela-S3	cervix:	n/a	chr11:9590549-9590564 chr11:9590552-9590561 chr11:9590547-9590563 chr11:9590550-9590564 chr11:9590548-9590562 chr11:9590381-9590395
44	STAT3	chr11:9590341-9590781	MCF10A-Er-Src	breast:	n/a	n/a
45	JUND	chr11:9589794-9590739	H1-hESC	embryonic stem cell:	n/a	n/a
46	NR3C1	chr11:9590363-9590854	ECC-1	luminal epithelium:	n/a	chr11:9590650-9590664 chr11:9590649-9590665 chr11:9590499-9590514 chr11:9590649-9590665 chr11:9590650-9590664 chr11:9590649-9590665 chr11:9590646-9590667 chr11:9590649-9590665
47	MAX	chr11:9590310-9591349	HepG2	liver:	n/a	n/a
48	CEBPB	chr11:9590319-9590767	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr11:9589767-9592014	MCF10A-Er-Src	breast:	n/a	n/a
50	MAX	chr11:9590265-9591287	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:9589863..9592978-chr11:9632988..9635615,3	K562	blood:
2	chr11:9589366..9592285-chr11:9609804..9612652,2	MCF-7	breast:
3	chr11:9482098..9486375-chr11:9587030..9591762,7	K562	blood:
4	chr11:9589955..9591769-chr11:9771252..9773790,2	MCF-7	breast:
5	chr11:9383299..9385895-chr11:9587946..9590537,2	MCF-7	breast:
6	chr11:9587790..9592116-chr11:9635065..9637852,3	MCF-7	breast:
7	chr11:9480903..9485608-chr11:9587733..9592274,8	MCF-7	breast:

Variant related genes	Relation type
WEE1	TF binding region
ENSG00000166478	Chromatin interaction
ENSG00000268403	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10840262	0.81[JPT][hapmap];0.80[TSI][hapmap];0.80[ASN][1000 genomes]
rs4910479	0.98[ASN][1000 genomes]
rs6486429	0.81[ASN][1000 genomes]
rs7937639	0.83[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs921678	0.95[JPT][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv553467	chr11:9518551-9648721	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7939541	TRIM22	cis	cerebellum	SCAN
rs7939541	SWAP70	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9584200-9594400	Enhancers	Stomach Mucosa	stomach
2	chr11:9584200-9594400	Weak transcription	Spleen	Spleen
3	chr11:9585200-9590800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr11:9585200-9593600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:9585200-9594400	Weak transcription	Esophagus	oesophagus
6	chr11:9585200-9594400	Weak transcription	Lung	lung
7	chr11:9586000-9591600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:9586200-9590400	Enhancers	Fetal Lung	lung
9	chr11:9586200-9590600	Enhancers	Hela-S3	cervix
10	chr11:9586200-9590600	Enhancers	NHLF	lung
11	chr11:9586400-9594200	Enhancers	Fetal Intestine Small	intestine
12	chr11:9586600-9590800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr11:9586600-9590800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:9586600-9591800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:9586600-9594000	Enhancers	Placenta	Placenta
16	chr11:9586600-9594200	Enhancers	Fetal Intestine Large	intestine
17	chr11:9586800-9590800	Weak transcription	Right Atrium	heart
18	chr11:9586800-9591000	Weak transcription	Right Ventricle	heart
19	chr11:9587000-9590800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:9588000-9590800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:9588000-9590800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr11:9588000-9590800	Weak transcription	Left Ventricle	heart
23	chr11:9588000-9591000	Genic enhancers	Duodenum Smooth Muscle	Duodenum
24	chr11:9588000-9594400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr11:9588000-9594400	Weak transcription	Gastric	stomach
26	chr11:9588200-9590400	Weak transcription	Fetal Muscle Leg	muscle
27	chr11:9588200-9590600	Weak transcription	Aorta	Aorta
28	chr11:9588200-9590600	Weak transcription	Small Intestine	intestine
29	chr11:9588200-9591200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr11:9588400-9590800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr11:9588600-9590400	Weak transcription	GM12878-XiMat	blood
32	chr11:9588600-9590600	Enhancers	K562	blood
33	chr11:9588600-9590600	Enhancers	NH-A	brain
34	chr11:9588600-9591200	Weak transcription	Psoas Muscle	Psoas
35	chr11:9588600-9593800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr11:9588600-9594000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr11:9588800-9590600	Enhancers	Fetal Heart	heart
38	chr11:9589400-9590400	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr11:9589400-9590600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr11:9589600-9590400	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr11:9589600-9590400	Enhancers	HSMM	muscle
42	chr11:9589600-9590400	Flanking Active TSS	NHEK	skin
43	chr11:9589600-9590600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr11:9589600-9590800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr11:9589600-9590800	Flanking Active TSS	Liver	Liver
46	chr11:9589600-9591600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr11:9589600-9591800	Enhancers	H1 Cell Line	embryonic stem cell
48	chr11:9589600-9591800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr11:9589600-9591800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:9589600-9591800	Enhancers	Fetal Stomach	stomach

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