Variant report

Variant	rs744172
Chromosome Location	chr1:59367040-59367041
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr1:59366742-59367128	HepG2	liver:	n/a	n/a
2	FOXA1	chr1:59366687-59367202	HepG2	liver:	n/a	chr1:59366714-59366726
3	RCOR1	chr1:59367033-59367415	K562	blood:	n/a	n/a
4	EP300	chr1:59366773-59367095	HepG2	liver:	n/a	n/a
5	FOXA1	chr1:59366712-59367191	HepG2	liver:	n/a	chr1:59366714-59366726
6	FOXA2	chr1:59366801-59367147	A549	lung:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:59366576..59370002-chr1:59372804..59375528,3	K562	blood:
2	chr1:59335945..59337936-chr1:59364743..59367099,2	K562	blood:
3	chr1:59242448..59252747-chr1:59356992..59375072,48	K562	blood:
4	chr1:59242448..59251438-chr1:59358057..59375559,39	K562	blood:
5	chr1:59365659..59367179-chr1:59378330..59379846,2	K562	blood:
6	chr1:59364854..59367542-chr1:59372083..59374801,2	K562	blood:
7	chr1:59248088..59252183-chr1:59365231..59372787,10	MCF-7	breast:
8	chr1:59285707..59288503-chr1:59364904..59368288,3	K562	blood:
9	chr1:59366023..59368709-chr1:59384060..59386406,2	K562	blood:
10	chr1:59247507..59253331-chr1:59366916..59371031,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000232453	TF binding region
ENSG00000234807	Chromatin interaction
ENSG00000177606	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12401645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12405442	0.91[AFR][1000 genomes]
rs1807117	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912380	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]

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	nsv1005354	chr1:59283572-59535812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv829959	chr1:59340330-59503085	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59356200-59368600	Weak transcription	Esophagus	oesophagus
2	chr1:59358200-59367200	Enhancers	HUVEC	blood vessel
3	chr1:59358400-59368600	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr1:59359000-59367200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr1:59359000-59368600	Enhancers	Fetal Intestine Small	intestine
6	chr1:59359000-59368800	Enhancers	Fetal Intestine Large	intestine
7	chr1:59361200-59368800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:59361600-59368400	Weak transcription	GM12878-XiMat	blood
9	chr1:59361800-59368800	Weak transcription	HMEC	breast
10	chr1:59362400-59368600	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr1:59362400-59368600	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr1:59362400-59368800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:59362400-59369000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:59362600-59368600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:59362600-59368800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:59362600-59368800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr1:59362800-59367800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:59362800-59367800	Weak transcription	Fetal Thymus	thymus
19	chr1:59362800-59368600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:59362800-59368600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:59362800-59368800	Weak transcription	NH-A	brain
22	chr1:59362800-59368800	Weak transcription	NHEK	skin
23	chr1:59362800-59369000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:59362800-59369000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:59363200-59368400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:59363200-59368600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:59363200-59369000	Weak transcription	Brain Angular Gyrus	brain
28	chr1:59364400-59367800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr1:59364600-59367200	Enhancers	Stomach Mucosa	stomach
30	chr1:59364600-59367600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:59364600-59368200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:59364600-59368800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:59364800-59368600	Enhancers	HepG2	liver
34	chr1:59365000-59368600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr1:59365200-59367200	Enhancers	HSMMtube	muscle
36	chr1:59365200-59368600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:59365200-59368800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:59365400-59368000	Weak transcription	Spleen	Spleen
39	chr1:59365400-59368800	Weak transcription	Aorta	Aorta
40	chr1:59365400-59369000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:59365400-59369000	Weak transcription	Right Ventricle	heart
42	chr1:59365400-59369200	Weak transcription	Gastric	stomach
43	chr1:59365600-59368400	Weak transcription	Liver	Liver
44	chr1:59365600-59368800	Weak transcription	Right Atrium	heart
45	chr1:59365600-59369000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr1:59365600-59369000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:59365600-59369000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:59365800-59367200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:59365800-59367200	Enhancers	A549	lung
50	chr1:59365800-59368800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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