Variant report

Variant	rs549538741
Chromosome Location	chr11:9594329-9594330
allele	C/G
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	chr11:9594236-9595686	PFSK-1	brain:	n/a	n/a
2	FOXA1	chr11:9594088-9595260	HepG2	liver:	n/a	n/a
3	POLR2A	chr11:9594325-9595577	HUVEC	blood vessel:	n/a	n/a
4	TAF1	chr11:9594283-9595978	ECC-1	luminal epithelium:	n/a	n/a
5	USF1	chr11:9594252-9594510	SK-N-SH_RA	brain:	n/a	n/a
6	MAX	chr11:9594224-9596603	GM12878	blood:	n/a	chr11:9594393-9594404 chr11:9594393-9594403 chr11:9595186-9595197 chr11:9595186-9595197 chr11:9595391-9595400 chr11:9594394-9594403 chr11:9595391-9595400 chr11:9594395-9594402 chr11:9594390-9594405 chr11:9595188-9595197 chr11:9594392-9594407 chr11:9595392-9595399
7	MAX	chr11:9594250-9595554	K562	blood:	n/a	chr11:9594393-9594404 chr11:9594393-9594403 chr11:9595186-9595197 chr11:9595186-9595197 chr11:9595391-9595400 chr11:9594394-9594403 chr11:9595391-9595400 chr11:9594395-9594402 chr11:9594390-9594405 chr11:9595188-9595197 chr11:9594392-9594407 chr11:9595392-9595399
8	MAX	chr11:9594248-9595832	K562	blood:	n/a	chr11:9594393-9594404 chr11:9594393-9594403 chr11:9595186-9595197 chr11:9595186-9595197 chr11:9595391-9595400 chr11:9594394-9594403 chr11:9595391-9595400 chr11:9594395-9594402 chr11:9594390-9594405 chr11:9595188-9595197 chr11:9594392-9594407 chr11:9595392-9595399
9	MYBL2	chr11:9594191-9595591	HepG2	liver:	n/a	n/a
10	USF2	chr11:9594208-9594556	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr11:9594277-9595726	GM12892	blood:	n/a	n/a
12	MXI1	chr11:9593222-9598393	SK-N-SH	brain:	n/a	n/a
13	USF1	chr11:9594134-9594563	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr11:9594208-9595540	U87	brain:	n/a	n/a
15	USF1	chr11:9594245-9594590	K562	blood:	n/a	n/a
16	MAX	chr11:9594223-9595573	HUVEC	blood vessel:	n/a	chr11:9594393-9594404 chr11:9594393-9594403 chr11:9595186-9595197 chr11:9595186-9595197 chr11:9595391-9595400 chr11:9594394-9594403 chr11:9595391-9595400 chr11:9594395-9594402 chr11:9594390-9594405 chr11:9595188-9595197 chr11:9594392-9594407 chr11:9595392-9595399
17	POLR2A	chr11:9594287-9597716	PBDE	blood:	n/a	n/a
18	NFIC	chr11:9594172-9595518	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr11:9593829-9601404	MCF10A-Er-Src	breast:	n/a	n/a
20	NFIC	chr11:9594166-9595416	ECC-1	luminal epithelium:	n/a	n/a
21	E2F6	chr11:9594200-9595394	A549	lung:	n/a	chr11:9595087-9595097 chr11:9595083-9595094 chr11:9595086-9595097 chr11:9595089-9595096 chr11:9595344-9595354 chr11:9595363-9595373 chr11:9595088-9595096 chr11:9595088-9595096 chr11:9595085-9595096 chr11:9595292-9595301 chr11:9595088-9595096 chr11:9595201-9595213
22	YY1	chr11:9594287-9594885	SK-N-SH	brain:	n/a	chr11:9594821-9594835 chr11:9594838-9594849 chr11:9594831-9594842
23	ELF1	chr11:9594317-9595394	K562	blood:	n/a	chr11:9595271-9595283 chr11:9595060-9595072 chr11:9595346-9595355 chr11:9594821-9594830 chr11:9595301-9595310
24	HEY1	chr11:9594201-9595598	HepG2	liver:	n/a	chr11:9595294-9595309 chr11:9595297-9595312 chr11:9595341-9595356 chr11:9594830-9594845
25	USF1	chr11:9594171-9594520	A549	lung:	n/a	n/a
26	SIN3AK20	chr11:9594290-9594960	HepG2	liver:	n/a	n/a
27	SIN3A	chr11:9594255-9595851	GM12878	blood:	n/a	chr11:9595382-9595393 chr11:9594766-9594779
28	USF1	chr11:9594243-9594734	SK-N-SH_RA	brain:	n/a	n/a
29	NR2F2	chr11:9594123-9595362	K562	blood:	n/a	n/a
30	MAX	chr11:9594214-9595556	HepG2	liver:	n/a	chr11:9594393-9594404 chr11:9594393-9594403 chr11:9595186-9595197 chr11:9595186-9595197 chr11:9595391-9595400 chr11:9594394-9594403 chr11:9595391-9595400 chr11:9594395-9594402 chr11:9594390-9594405 chr11:9595188-9595197 chr11:9594392-9594407 chr11:9595392-9595399
31	POLR2A	chr11:9594122-9595677	U87	brain:	n/a	n/a
32	POLR2A	chr11:9593092-9599445	IMR90	lung:	n/a	n/a
33	MYC	chr11:9594296-9595420	HepG2	liver:	n/a	chr11:9594393-9594404 chr11:9594393-9594403 chr11:9595186-9595197 chr11:9595186-9595197 chr11:9595391-9595400 chr11:9594394-9594403 chr11:9595391-9595400 chr11:9594395-9594402 chr11:9594390-9594405 chr11:9595188-9595197 chr11:9594392-9594407 chr11:9595392-9595399
34	MBD4	chr11:9594203-9594653	HepG2	liver:	n/a	n/a
35	POLR2A	chr11:9594264-9595673	GM12878	blood:	n/a	n/a
36	USF2	chr11:9594237-9594563	H1-hESC	embryonic stem cell:	n/a	n/a
37	POU2F2	chr11:9594322-9595063	GM12891	blood:	n/a	n/a
38	POLR2A	chr11:9594253-9595709	MCF-7	breast:	n/a	n/a
39	TAF1	chr11:9594282-9595710	ECC-1	luminal epithelium:	n/a	n/a
40	TCF7L2	chr11:9594268-9595933	PANC-1	pancreas:	n/a	n/a
41	SIN3AK20	chr11:9593713-9597257	PANC-1	pancreas:	n/a	n/a
42	GABPA	chr11:9594247-9595211	SK-N-SH	brain:	n/a	n/a
43	SIN3AK20	chr11:9594246-9595003	PANC-1	pancreas:	n/a	n/a
44	POLR2A	chr11:9594027-9595660	K562	blood:	n/a	n/a
45	TCF12	chr11:9594270-9595539	ECC-1	luminal epithelium:	n/a	n/a
46	MAX	chr11:9594143-9595653	MCF-7	breast:	n/a	chr11:9594393-9594404 chr11:9594393-9594403 chr11:9595186-9595197 chr11:9595186-9595197 chr11:9595391-9595400 chr11:9594394-9594403 chr11:9595391-9595400 chr11:9594395-9594402 chr11:9594390-9594405 chr11:9595188-9595197 chr11:9594392-9594407 chr11:9595392-9595399
47	YY1	chr11:9594264-9594911	ECC-1	luminal epithelium:	n/a	chr11:9594821-9594835 chr11:9594838-9594849 chr11:9594831-9594842
48	UBTF	chr11:9594271-9597345	K562	blood:	n/a	n/a
49	CHD2	chr11:9594272-9595528	HepG2	liver:	n/a	n/a
50	POLR2A	chr11:9594225-9595461	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:9112943..9114701-chr11:9593377..9596594,3	MCF-7	breast:
2	chr11:9594244..9596039-chr11:9777459..9779743,2	MCF-7	breast:
3	chr11:9479099..9485582-chr11:9593306..9599058,18	K562	blood:
4	chr11:9482166..9483015-chr11:9594207..9594915,2	Hela-S3	cervix:
5	chr11:8702253..8704416-chr11:9593339..9594880,2	MCF-7	breast:
6	chr11:9593380..9601954-chr11:9626466..9639393,32	K562	blood:
7	chr11:9571322..9573839-chr11:9593135..9594742,2	K562	blood:
8	chr11:9478618..9485582-chr11:9593299..9599536,13	K562	blood:
9	chr11:9480226..9484903-chr11:9591788..9598525,12	MCF-7	breast:
10	chr11:9593146..9594870-chr11:9635191..9636726,2	MCF-7	breast:
11	chr11:9594272..9594821-chr17:25621066..25621930,2	Hela-S3	cervix:

Variant related genes	Relation type
WEE1	TF binding region
ENSG00000245522	Chromatin interaction
ENSG00000243964	Chromatin interaction
ENSG00000166441	Chromatin interaction
ENSG00000166478	Chromatin interaction
ENSG00000109046	Chromatin interaction
ENSG00000175356	Chromatin interaction
ENSG00000268403	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	esv3365334	chr11:9593876-9597474	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
4	esv3439005	chr11:9593901-9596949	Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 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	chr11:9585200-9594400	Weak transcription	Esophagus	oesophagus
4	chr11:9585200-9594400	Weak transcription	Lung	lung
5	chr11:9588000-9594400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr11:9588000-9594400	Weak transcription	Gastric	stomach
7	chr11:9591000-9594400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:9591200-9594400	Weak transcription	Pancreas	Pancrea
9	chr11:9591600-9594400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:9591600-9594600	Weak transcription	Small Intestine	intestine
11	chr11:9591600-9596200	Weak transcription	Fetal Heart	heart
12	chr11:9592200-9594400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:9593600-9595800	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr11:9593600-9596200	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr11:9593600-9596600	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr11:9593600-9598000	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr11:9593800-9594400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr11:9593800-9594400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr11:9593800-9594400	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr11:9593800-9594600	Flanking Active TSS	Fetal Muscle Trunk	muscle
21	chr11:9593800-9594600	Flanking Active TSS	Fetal Muscle Leg	muscle
22	chr11:9593800-9594600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr11:9593800-9594600	Flanking Active TSS	Dnd41	blood
24	chr11:9593800-9594800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:9593800-9594800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr11:9593800-9596400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:9593800-9596400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:9593800-9596400	Active TSS	HepG2	liver
29	chr11:9593800-9596400	Active TSS	Osteobl	bone
30	chr11:9593800-9596600	Active TSS	Brain Hippocampus Middle	brain
31	chr11:9593800-9597200	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr11:9593800-9597400	Active TSS	A549	lung
33	chr11:9593800-9597800	Active TSS	H1 Cell Line	embryonic stem cell
34	chr11:9593800-9598200	Active TSS	H9 Cell Line	embryonic stem cell
35	chr11:9593800-9599000	Active TSS	Psoas Muscle	Psoas
36	chr11:9593800-9599600	Active TSS	Brain Germinal Matrix	brain
37	chr11:9593800-9599800	Active TSS	HSMMtube	muscle
38	chr11:9594000-9594400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr11:9594000-9594400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr11:9594000-9594400	Active TSS	NH-A	brain
41	chr11:9594000-9594600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr11:9594000-9594600	Active TSS	Stomach Smooth Muscle	stomach
43	chr11:9594000-9594800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr11:9594000-9594800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr11:9594000-9594800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr11:9594000-9594800	Flanking Active TSS	Placenta	Placenta
47	chr11:9594000-9594800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr11:9594000-9595000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr11:9594000-9595000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:9594000-9596200	Active TSS	Adipose Nuclei	Adipose

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