Variant report

Variant	rs11957249
Chromosome Location	chr5:53685902-53685903
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	chr5:53685882-53686158	MCF10A-Er-Src	breast:	n/a	n/a
2	RFX5	chr5:53685850-53686283	Hela-S3	cervix:	n/a	chr5:53686087-53686095
3	GATA3	chr5:53685663-53686434	SK-N-SH	brain:	n/a	n/a
4	FOS	chr5:53685766-53686166	MCF10A-Er-Src	breast:	n/a	chr5:53686001-53686010
5	POLR2A	chr5:53685757-53686268	U87	brain:	n/a	n/a
6	MAX	chr5:53685719-53686271	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr5:53685763-53686262	U87	brain:	n/a	n/a
8	MYC	chr5:53685725-53686167	MCF10A-Er-Src	breast:	n/a	n/a
9	RCOR1	chr5:53685825-53686728	K562	blood:	n/a	n/a
10	JUND	chr5:53685860-53686186	A549	lung:	n/a	chr5:53686001-53686010
11	RCOR1	chr5:53685881-53686245	K562	blood:	n/a	n/a
12	POLR2A	chr5:53685828-53686163	K562	blood:	n/a	n/a
13	KAP1	chr5:53685727-53687014	HEK293	kidney:	n/a	n/a
14	EP300	chr5:53685827-53686234	Hela-S3	cervix:	n/a	n/a
15	JUN	chr5:53685795-53686668	K562	blood:	n/a	chr5:53686001-53686010
16	MYC	chr5:53685825-53686175	K562	blood:	n/a	n/a
17	JUN	chr5:53685822-53686194	K562	blood:	n/a	chr5:53686001-53686010
18	USF2	chr5:53685897-53686100	Hela-S3	cervix:	n/a	n/a
19	FOSL2	chr5:53685777-53686321	SK-N-SH	brain:	n/a	chr5:53686001-53686010
20	RAD21	chr5:53685853-53686103	SK-N-SH_RA	brain:	n/a	n/a
21	TCF7L2	chr5:53685835-53686605	HEK293	kidney:	n/a	chr5:53686419-53686435 chr5:53686421-53686431 chr5:53686420-53686434 chr5:53686419-53686435
22	EP300	chr5:53685826-53686146	SK-N-SH_RA	brain:	n/a	n/a
23	SETDB1	chr5:53685826-53686333	U2OS	brain:	n/a	n/a
24	JUN	chr5:53685346-53687377	K562	blood:	n/a	chr5:53686001-53686010
25	PBX3	chr5:53685654-53686195	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr5:53685789-53686192	U87	brain:	n/a	n/a
27	JUND	chr5:53685789-53686849	K562	blood:	n/a	chr5:53686001-53686010
28	ZNF263	chr5:53685754-53686518	HEK293-T-REx	kidney:	n/a	n/a
29	ATF3	chr5:53685810-53686230	K562	blood:	n/a	chr5:53685998-53686013
30	SP1	chr5:53685773-53686137	A549	lung:	n/a	n/a
31	ATF1	chr5:53685785-53686164	K562	blood:	n/a	n/a
32	TBL1XR1	chr5:53685710-53686843	K562	blood:	n/a	n/a
33	GATA2	chr5:53685782-53686228	K562	blood:	n/a	n/a
34	FOS	chr5:53685733-53686187	MCF10A-Er-Src	breast:	n/a	chr5:53686001-53686010
35	GATA3	chr5:53685778-53686205	T-47D	breast:	n/a	n/a
36	MAX	chr5:53685823-53686127	K562	blood:	n/a	n/a
37	TBL1XR1	chr5:53685805-53686174	K562	blood:	n/a	n/a
38	EP300	chr5:53685722-53686895	K562	blood:	n/a	n/a
39	FOXA1	chr5:53685789-53686104	T-47D	breast:	n/a	chr5:53685831-53685843
40	FOXA1	chr5:53685787-53686171	T-47D	breast:	n/a	chr5:53685831-53685843
41	PBX3	chr5:53685783-53686317	SK-N-SH	brain:	n/a	n/a
42	MEF2A	chr5:53685797-53686300	SK-N-SH	brain:	n/a	n/a
43	RAD21	chr5:53685837-53686107	SK-N-SH_RA	brain:	n/a	n/a
44	TAL1	chr5:53685847-53686588	K562	blood:	n/a	n/a
45	GATA3	chr5:53685676-53686396	SK-N-SH	brain:	n/a	n/a
46	JUND	chr5:53685613-53686290	SK-N-SH	brain:	n/a	chr5:53686001-53686010
47	SMARCB1	chr5:53685848-53686765	K562	blood:	n/a	n/a
48	GATA3	chr5:53685771-53686155	MCF-7	breast:	n/a	n/a
49	CBX3	chr5:53685718-53686211	K562	blood:	n/a	n/a
50	ZNF143	chr5:53685791-53686110	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:53666534..53671507-chr5:53683595..53686253,5	K562	blood:
2	chr5:53623630..53625558-chr5:53684671..53686231,2	MCF-7	breast:
3	chr5:53605853..53609954-chr5:53683812..53688635,7	K562	blood:
4	chr5:53604135..53610802-chr5:53683563..53694160,14	K562	blood:
5	chr5:53620244..53622650-chr5:53684133..53686111,2	K562	blood:
6	chr5:53684453..53686061-chr5:53689713..53692526,2	K562	blood:

Variant related genes	Relation type
LINC01033	TF binding region
ENSG00000249069	Chromatin interaction
ENSG00000185305	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10041550	1.00[ASN][1000 genomes]
rs10041555	1.00[ASN][1000 genomes]
rs10043654	1.00[ASN][1000 genomes]
rs10074776	1.00[ASN][1000 genomes]
rs11739911	1.00[ASN][1000 genomes]
rs11740324	1.00[ASN][1000 genomes]
rs11743996	1.00[ASN][1000 genomes]
rs13155990	1.00[ASN][1000 genomes]
rs13156373	1.00[ASN][1000 genomes]
rs13157497	1.00[ASN][1000 genomes]
rs13159846	1.00[ASN][1000 genomes]
rs13162552	1.00[ASN][1000 genomes]
rs13171042	1.00[ASN][1000 genomes]
rs13182438	1.00[ASN][1000 genomes]
rs13183386	1.00[ASN][1000 genomes]
rs13190010	1.00[ASN][1000 genomes]
rs13354296	1.00[ASN][1000 genomes]
rs13354604	1.00[ASN][1000 genomes]
rs13356576	1.00[ASN][1000 genomes]
rs16882546	1.00[ASN][1000 genomes]
rs16882575	1.00[ASN][1000 genomes]
rs16882580	1.00[ASN][1000 genomes]
rs16882609	1.00[ASN][1000 genomes]
rs17321792	1.00[ASN][1000 genomes]
rs34171374	1.00[ASN][1000 genomes]
rs34430216	1.00[ASN][1000 genomes]
rs34883270	1.00[ASN][1000 genomes]
rs34889997	1.00[ASN][1000 genomes]
rs35486183	1.00[ASN][1000 genomes]
rs35503723	1.00[ASN][1000 genomes]
rs35646158	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35702491	1.00[ASN][1000 genomes]
rs35765393	1.00[ASN][1000 genomes]
rs36104210	1.00[ASN][1000 genomes]
rs62355131	1.00[ASN][1000 genomes]
rs6450182	1.00[ASN][1000 genomes]
rs67009061	1.00[ASN][1000 genomes]
rs67012013	1.00[ASN][1000 genomes]
rs67089826	1.00[ASN][1000 genomes]
rs67894567	1.00[ASN][1000 genomes]
rs6859542	1.00[ASN][1000 genomes]
rs6891928	1.00[ASN][1000 genomes]
rs6892938	1.00[ASN][1000 genomes]
rs71622108	1.00[ASN][1000 genomes]
rs71622110	1.00[ASN][1000 genomes]
rs72752163	1.00[ASN][1000 genomes]
rs72757857	1.00[ASN][1000 genomes]
rs73120767	1.00[ASN][1000 genomes]
rs7704922	1.00[ASN][1000 genomes]
rs7733332	1.00[ASN][1000 genomes]
rs9292043	1.00[ASN][1000 genomes]
rs9292044	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv881018	chr5:53305742-53744849	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
3	nsv880734	chr5:53305742-53770217	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
4	nsv881161	chr5:53305742-53815495	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
5	nsv881600	chr5:53305742-53823285	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
6	nsv598176	chr5:53311502-53739530	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
7	nsv880773	chr5:53311918-53815495	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1024303	chr5:53317896-53788276	Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1029224	chr5:53317896-53812899	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv949098	chr5:53317990-53816782	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
11	nsv1020517	chr5:53324930-53759046	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1017768	chr5:53326385-53752165	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
13	nsv1032352	chr5:53327170-53762973	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
14	nsv598177	chr5:53333477-53755208	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
15	nsv881056	chr5:53368869-53744849	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
16	nsv881408	chr5:53386267-53815495	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv1031072	chr5:53490130-53698866	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv880304	chr5:53524508-53727092	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	nsv880904	chr5:53574006-53737364	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53682200-53687200	Genic enhancers	K562	blood
2	chr5:53682600-53686000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:53683000-53686200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:53683200-53686400	Enhancers	HSMM	muscle
5	chr5:53683400-53686400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:53683400-53686600	Enhancers	Muscle Satellite Cultured Cells	--
7	chr5:53684600-53690400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr5:53685200-53686200	Enhancers	HMEC	breast
9	chr5:53685400-53686400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:53685400-53686400	Enhancers	NHEK	skin
11	chr5:53685600-53686200	Enhancers	NHDF-Ad	bronchial
12	chr5:53685600-53686400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:53685800-53686000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr5:53685800-53686000	Enhancers	HSMMtube	muscle
15	chr5:53685800-53686200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:53685800-53686200	Enhancers	Fetal Heart	heart
17	chr5:53685800-53686200	Enhancers	Fetal Kidney	kidney
18	chr5:53685800-53686200	Enhancers	Fetal Muscle Leg	muscle
19	chr5:53685800-53686200	Enhancers	NHLF	lung
20	chr5:53685800-53686200	Enhancers	Osteobl	bone
21	chr5:53685800-53686400	Enhancers	Fetal Intestine Large	intestine
22	chr5:53685800-53686600	Enhancers	Hela-S3	cervix
23	chr5:53685800-53686600	Enhancers	NH-A	brain
24	chr5:53685800-53686800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:53685800-53686800	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr5:53685800-53687200	Enhancers	Cortex derived primary cultured neurospheres	brain

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