Variant report

Variant	rs72717527
Chromosome Location	chr1:179333952-179333953
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:179333806-179335727	GM12891	blood:	n/a	n/a
2	POLR2A	chr1:179333903-179335412	GM19193	blood:	n/a	n/a
3	POLR2A	chr1:179333749-179334016	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:179049160..179052033-chr1:179333339..179335895,3	K562	blood:
2	chr1:179332952..179336574-chr1:179337996..179342859,7	MCF-7	breast:
3	chr1:179260885..179265137-chr1:179333383..179339387,7	MCF-7	breast:
4	chr1:179049954..179052769-chr1:179333565..179337813,7	MCF-7	breast:
5	chr1:179048972..179052099-chr1:179331450..179336701,5	MCF-7	breast:
6	chr1:179333390..179336673-chr1:179338029..179341473,3	MCF-7	breast:

No data

Variant related genes	Relation type
AXDND1	TF binding region
ENSG00000057252	Chromatin interaction
ENSG00000186283	Chromatin interaction
ENSG00000162779	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11802378	1.00[AFR][1000 genomes]
rs11802834	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11805319	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11805875	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11807230	1.00[AFR][1000 genomes]
rs11807253	1.00[AFR][1000 genomes]
rs11809032	1.00[AFR][1000 genomes]
rs11809095	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs16854006	0.97[EUR][1000 genomes]
rs2209923	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2209924	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs28914473	1.00[AFR][1000 genomes]
rs28991582	1.00[AFR][1000 genomes]
rs60890328	0.92[EUR][1000 genomes]
rs72704430	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs72704457	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs72704464	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs72704465	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs72704468	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs72709467	1.00[AFR][1000 genomes]
rs72709474	1.00[AFR][1000 genomes]
rs72709475	1.00[AFR][1000 genomes]
rs72709477	1.00[AFR][1000 genomes]
rs72709479	1.00[AFR][1000 genomes]
rs72709481	1.00[AFR][1000 genomes]
rs72709485	1.00[AFR][1000 genomes]
rs72709486	1.00[AFR][1000 genomes]
rs72709487	1.00[AFR][1000 genomes]
rs72709488	1.00[AFR][1000 genomes]
rs72709490	1.00[AFR][1000 genomes]
rs72709492	1.00[AFR][1000 genomes]
rs72709493	1.00[AFR][1000 genomes]
rs72709494	1.00[AFR][1000 genomes]
rs72709495	1.00[AFR][1000 genomes]
rs72709497	1.00[AFR][1000 genomes]
rs72711608	1.00[AFR][1000 genomes]
rs72711609	1.00[AFR][1000 genomes]
rs72711612	1.00[AFR][1000 genomes]
rs72711615	1.00[AFR][1000 genomes]
rs72713484	1.00[AFR][1000 genomes]
rs72713485	1.00[AFR][1000 genomes]
rs72713494	1.00[AFR][1000 genomes]
rs72715506	1.00[AFR][1000 genomes]
rs72715515	1.00[AFR][1000 genomes]
rs72715520	1.00[AFR][1000 genomes]
rs72715533	1.00[AFR][1000 genomes]
rs72715595	1.00[AFR][1000 genomes]
rs72715597	1.00[AFR][1000 genomes]
rs72715599	1.00[AFR][1000 genomes]
rs72717511	0.92[EUR][1000 genomes]
rs72717517	0.97[EUR][1000 genomes]
rs72717520	0.97[EUR][1000 genomes]
rs72717523	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72717535	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72717536	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72719210	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72719259	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2762031	chr1:179323738-179375197	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
3	nsv518403	chr1:179323919-179371973	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv548279	chr1:179323919-179390148	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3523650	chr1:179328529-179335027	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	esv33901	chr1:179328708-179344905	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	esv3523651	chr1:179328979-179334877	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	esv3523653	chr1:179328979-179334877	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	esv20900	chr1:179329828-179335094	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	nsv548284	chr1:179329899-179334801	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
11	nsv548285	chr1:179329899-179334934	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
12	esv3371887	chr1:179330029-179334927	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
13	nsv548289	chr1:179330173-179334801	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
14	nsv548292	chr1:179330576-179334801	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
15	nsv548294	chr1:179330932-179334801	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
16	nsv548296	chr1:179330984-179334801	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179264800-179334200	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:179300400-179334600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:179305600-179334200	Weak transcription	Pancreas	Pancrea
4	chr1:179312600-179334400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:179314800-179334400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:179315000-179334400	Weak transcription	Brain Substantia Nigra	brain
7	chr1:179315000-179334400	Weak transcription	Left Ventricle	heart
8	chr1:179315400-179334400	Weak transcription	Fetal Kidney	kidney
9	chr1:179315600-179334400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:179315800-179334200	Weak transcription	Fetal Thymus	thymus
11	chr1:179316000-179334000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:179316000-179334200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:179316000-179334400	Weak transcription	Fetal Brain Female	brain
14	chr1:179316000-179334400	Weak transcription	Ovary	ovary
15	chr1:179317600-179334400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:179319200-179334400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:179319800-179334000	Weak transcription	HepG2	liver
18	chr1:179319800-179334200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:179320000-179334600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:179320800-179334000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:179320800-179334200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:179320800-179334400	Weak transcription	Fetal Lung	lung
23	chr1:179321000-179334200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:179321200-179334400	Weak transcription	Fetal Stomach	stomach
25	chr1:179321200-179334400	Weak transcription	Lung	lung
26	chr1:179322400-179334200	Weak transcription	Primary B cells from cord blood	blood
27	chr1:179323000-179334200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:179323000-179334200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:179323000-179334200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:179323000-179334400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:179323000-179334400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:179323000-179334400	Weak transcription	NH-A	brain
33	chr1:179323000-179334400	Weak transcription	Osteobl	bone
34	chr1:179323200-179334200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:179323200-179334200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr1:179323200-179334200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:179323200-179334200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:179323200-179334200	Weak transcription	A549	lung
39	chr1:179323200-179334400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:179323200-179334400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:179323200-179334400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr1:179323200-179334400	Weak transcription	Fetal Heart	heart
43	chr1:179323200-179334400	Weak transcription	Fetal Intestine Large	intestine
44	chr1:179323400-179334000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:179323400-179334200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr1:179323600-179334400	Weak transcription	NHLF	lung
47	chr1:179324000-179334200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:179324200-179334000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:179324200-179334000	Weak transcription	Dnd41	blood
50	chr1:179324200-179334200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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