Variant report

Variant	rs1001242
Chromosome Location	chr6:149773721-149773722
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZBTB7A	chr6:149773299-149773936	ECC-1	luminal epithelium:	n/a	n/a
2	ESR1	chr6:149773364-149773816	ECC-1	luminal epithelium:	n/a	n/a
3	ESR1	chr6:149773317-149773816	ECC-1	luminal epithelium:	n/a	n/a
4	CEBPB	chr6:149773526-149773769	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr6:149773558-149773947	GM12878	blood:	n/a	n/a
6	ESR1	chr6:149773436-149773808	ECC-1	luminal epithelium:	n/a	n/a
7	NFIC	chr6:149773250-149773960	ECC-1	luminal epithelium:	n/a	n/a
8	TCF12	chr6:149773305-149774003	ECC-1	luminal epithelium:	n/a	n/a
9	TCF12	chr6:149773216-149773925	ECC-1	luminal epithelium:	n/a	n/a
10	MAX	chr6:149773388-149773906	ECC-1	luminal epithelium:	n/a	n/a
11	EP300	chr6:149773322-149773993	ECC-1	luminal epithelium:	n/a	n/a
12	NFIC	chr6:149773245-149774035	ECC-1	luminal epithelium:	n/a	n/a
13	CEBPB	chr6:149773402-149773753	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:149767445..149770252-chr6:149772541..149774258,2	MCF-7	breast:
2	chr6:149769726..149773853-chr6:149775332..149778151,3	K562	blood:
3	chr6:149399709..149402380-chr6:149772394..149774498,2	K562	blood:

No data

Variant related genes	Relation type
ZC3H12D	TF binding region
ENSG00000178199	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1074495	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1339185	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1934117	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2007062	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2153219	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2744430	0.87[ASN][1000 genomes]
rs2789493	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2789495	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2789496	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2789498	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2789501	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3765290	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs475681	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4897125	0.83[ASN][1000 genomes]
rs512685	0.92[EUR][1000 genomes]
rs556775	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs587155	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62441728	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs632360	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs634440	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs656461	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs664951	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs760897	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs805027	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs909793	0.95[EUR][1000 genomes]
rs9377218	0.95[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	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv470866	chr6:149744632-149806552	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv5533	chr6:149748047-149793072	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv464076	chr6:149755695-149798835	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv604846	chr6:149755695-149798835	ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3355637	chr6:149769659-149774457	Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv3358166	chr6:149771284-149774132	Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149768400-149779400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:149769600-149782800	Strong transcription	Primary B cells from peripheral blood	blood
3	chr6:149769600-149787200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:149769800-149779800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:149770000-149779600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:149770000-149785200	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:149771600-149778000	Weak transcription	GM12878-XiMat	blood
8	chr6:149771800-149775600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:149771800-149775800	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr6:149772000-149788800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr6:149772200-149774000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr6:149772200-149775200	Strong transcription	Spleen	Spleen
13	chr6:149772200-149776600	Enhancers	Liver	Liver
14	chr6:149772400-149774000	Enhancers	Lung	lung
15	chr6:149772400-149774400	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr6:149772400-149776600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr6:149772400-149776600	Enhancers	Fetal Lung	lung
18	chr6:149772600-149773800	Enhancers	Pancreas	Pancrea
19	chr6:149772600-149774000	Enhancers	Stomach Mucosa	stomach
20	chr6:149772600-149774800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:149772600-149774800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr6:149772600-149775000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:149772600-149776400	Enhancers	Small Intestine	intestine
24	chr6:149772600-149779400	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr6:149772600-149787000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:149772800-149773800	Enhancers	Brain Anterior Caudate	brain
27	chr6:149772800-149773800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
28	chr6:149772800-149773800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
29	chr6:149772800-149773800	Enhancers	HepG2	liver
30	chr6:149772800-149774600	Enhancers	Right Ventricle	heart
31	chr6:149772800-149774800	Weak transcription	Aorta	Aorta
32	chr6:149772800-149774800	Enhancers	Stomach Smooth Muscle	stomach
33	chr6:149772800-149775000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:149772800-149775000	Weak transcription	Psoas Muscle	Psoas
35	chr6:149772800-149776400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr6:149773000-149774000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
37	chr6:149773000-149774600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:149773000-149774600	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr6:149773000-149774800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:149773000-149774800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:149773000-149774800	Weak transcription	Colon Smooth Muscle	Colon
42	chr6:149773000-149775000	Weak transcription	Left Ventricle	heart
43	chr6:149773000-149776800	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr6:149773000-149778200	Weak transcription	Thymus	Thymus
45	chr6:149773000-149779600	Weak transcription	Primary T cells from cord blood	blood
46	chr6:149773000-149783400	Strong transcription	Primary B cells from cord blood	blood
47	chr6:149773200-149773800	Enhancers	Fetal Intestine Large	intestine
48	chr6:149773200-149774200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr6:149773200-149774200	Weak transcription	Ovary	ovary
50	chr6:149773200-149774800	Enhancers	Hela-S3	cervix

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