Variant report

Variant	rs73498471
Chromosome Location	chr11:65813049-65813050
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	CTCF	chr11:65813016-65813133	GM19239	blood:	n/a	chr11:65813054-65813062
2	YY1	chr11:65812522-65813189	H1-hESC	embryonic stem cell:	n/a	chr11:65812748-65812757
3	STAT5A	chr11:65812402-65813108	GM12878	blood:	n/a	n/a
4	CTCF	chr11:65813026-65813093	GM12891	blood:	n/a	chr11:65813054-65813062
5	SMC3	chr11:65812470-65813127	SK-N-SH	brain:	n/a	n/a
6	HDAC2	chr11:65812466-65813068	MCF-7	breast:	n/a	n/a
7	CTCF	chr11:65813026-65813164	GM12892	blood:	n/a	chr11:65813054-65813062
8	CTCF	chr11:65812583-65813139	K562	blood:	n/a	chr11:65813054-65813062
9	CTCF	chr11:65812478-65813058	MCF-7	breast:	n/a	n/a
10	CTCF	chr11:65812485-65813090	MCF-7	breast:	n/a	chr11:65813054-65813062
11	RAD21	chr11:65812545-65813070	MCF-7	breast:	n/a	chr11:65812735-65812745 chr11:65813024-65813036
12	MAX	chr11:65812436-65813184	MCF-7	breast:	n/a	chr11:65813062-65813071
13	RCOR1	chr11:65812263-65813088	IMR90	lung:	n/a	n/a
14	MAZ	chr11:65811971-65813510	IMR90	lung:	n/a	chr11:65813062-65813071
15	CTCF	chr11:65812089-65813208	A549	lung:	n/a	chr11:65813054-65813062
16	ELF1	chr11:65812533-65813090	GM12878	blood:	n/a	n/a
17	CTCF	chr11:65813034-65813159	GM19238	blood:	n/a	chr11:65813054-65813062
18	TCF12	chr11:65812522-65813081	A549	lung:	n/a	n/a
19	ELF1	chr11:65812501-65813160	MCF-7	breast:	n/a	n/a
20	SP1	chr11:65812484-65813052	A549	lung:	n/a	chr11:65812715-65812728 chr11:65812746-65812758 chr11:65812747-65812757 chr11:65812746-65812758 chr11:65812747-65812756 chr11:65812718-65812729 chr11:65812747-65812756 chr11:65812747-65812761 chr11:65812746-65812757 chr11:65812748-65812757 chr11:65812747-65812757
21	CTCF	chr11:65812320-65813298	HCT-116	colon:	n/a	chr11:65813054-65813062
22	CTCF	chr11:65812980-65813130	GM12871	blood:	n/a	chr11:65813054-65813062
23	CTCF	chr11:65812162-65813320	SK-N-SH	brain:	n/a	chr11:65813054-65813062
24	HDAC2	chr11:65812474-65813058	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65812285..65813209-chr11:66025403..66026314,2	MCF-7	breast:
2	chr11:65812475..65816551-chr11:65816982..65820716,11	MCF-7	breast:
3	chr11:65657526..65660220-chr11:65812973..65815737,3	MCF-7	breast:
4	chr11:65792176..65796965-chr11:65812595..65817477,5	MCF-7	breast:
5	chr11:65767772..65771693-chr11:65812597..65815090,3	MCF-7	breast:
6	chr11:65812922..65815510-chr11:65837744..65839701,2	K562	blood:
7	chr11:65811021..65815121-chr11:65816503..65821449,7	K562	blood:
8	chr11:65787106..65790003-chr11:65812691..65814392,2	MCF-7	breast:

Variant related genes	Relation type
GAL3ST3	TF binding region
ENSG00000175229	Chromatin interaction
ENSG00000175294	Chromatin interaction
ENSG00000238752	Chromatin interaction
ENSG00000087365	Chromatin interaction
ENSG00000175115	Chromatin interaction
ENSG00000175602	Chromatin interaction
ENSG00000175376	Chromatin interaction
ENSG00000175334	Chromatin interaction
ENSG00000174996	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1143916	1.00[AMR][1000 genomes]
rs1144796	1.00[AMR][1000 genomes]
rs1151508	1.00[AMR][1000 genomes]
rs1191715	1.00[AMR][1000 genomes]
rs1201503	1.00[AMR][1000 genomes]
rs1203799	1.00[AMR][1000 genomes]
rs1630638	1.00[AMR][1000 genomes]
rs1783562	1.00[AMR][1000 genomes]
rs4930332	1.00[AMR][1000 genomes]
rs59973646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6591196	1.00[AMR][1000 genomes]
rs7947668	1.00[AMR][1000 genomes]
rs948477	1.00[AMR][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	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	nsv897768	chr11:65715210-65842064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription 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	61 gene(s)	inside rSNPs	diseases
3	nsv897769	chr11:65727799-65828625	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
4	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv897770	chr11:65803750-65824472	Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65790400-65818600	Weak transcription	HSMM	muscle
2	chr11:65805000-65815800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:65809800-65815800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:65811600-65814400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr11:65811800-65814200	Weak transcription	Brain Germinal Matrix	brain
6	chr11:65811800-65814600	Weak transcription	Fetal Brain Female	brain
7	chr11:65812000-65813400	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr11:65812200-65813200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr11:65812200-65813200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr11:65812200-65813200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr11:65812200-65814800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:65812400-65813200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr11:65812400-65813200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr11:65812400-65813200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:65812400-65813200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr11:65812400-65813200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr11:65812400-65813200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:65812400-65813200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr11:65812400-65813200	Enhancers	Primary hematopoietic stem cells	blood
20	chr11:65812400-65813200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr11:65812400-65813200	Enhancers	Muscle Satellite Cultured Cells	--
22	chr11:65812400-65813200	Enhancers	Adipose Nuclei	Adipose
23	chr11:65812400-65813200	Enhancers	Fetal Muscle Trunk	muscle
24	chr11:65812400-65813200	Enhancers	Fetal Thymus	thymus
25	chr11:65812400-65813200	Enhancers	Pancreas	Pancrea
26	chr11:65812400-65813200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr11:65812400-65813200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr11:65812400-65813400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr11:65812400-65813400	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr11:65812400-65813400	Enhancers	Primary T cells fromperipheralblood	blood
31	chr11:65812400-65813400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr11:65812400-65813400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr11:65812400-65813400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr11:65812400-65813400	Flanking Active TSS	Dnd41	blood
35	chr11:65812400-65813600	Enhancers	H1 Cell Line	embryonic stem cell
36	chr11:65812400-65813600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr11:65812400-65813600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr11:65812400-65813600	Enhancers	Brain Cingulate Gyrus	brain
39	chr11:65812400-65814600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr11:65812400-65815200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr11:65812600-65813200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr11:65812600-65813200	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr11:65812600-65813200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:65812600-65813200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr11:65812600-65813200	Enhancers	Duodenum Mucosa	Duodenum
46	chr11:65812600-65813200	Enhancers	Esophagus	oesophagus
47	chr11:65812600-65813200	Enhancers	Spleen	Spleen
48	chr11:65812600-65814400	Enhancers	Fetal Intestine Small	intestine
49	chr11:65812800-65813200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr11:65812800-65813200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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