Variant report

Variant	rs10915853
Chromosome Location	chr1:225842390-225842391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:225838660-225844042	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:225840071-225843898	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr1:225839159-225842396	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:225840526-225842504	U87	brain:	n/a	n/a
5	POLR2A	chr1:225839363-225842398	IMR90	lung:	n/a	n/a
6	POLR2A	chr1:225842253-225842390	MCF-7	breast:	n/a	n/a
7	POLR2A	chr1:225840532-225842504	U87	brain:	n/a	n/a
8	POLR2A	chr1:225838940-225842419	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:225841590..225843627-chr1:225887293..225890031,4	MCF-7	breast:
2	chr1:225839962..225842492-chr1:226249684..226252539,2	MCF-7	breast:
3	chr1:225842059..225843604-chr1:225963580..225966384,2	K562	blood:
4	chr1:225839775..225842863-chr1:225886341..225888955,3	MCF-7	breast:
5	chr1:225841158..225843185-chr1:226308432..226310542,2	MCF-7	breast:
6	chr1:225839309..225842570-chr1:226062972..226068660,6	MCF-7	breast:
7	chr1:225840996..225843850-chr1:225947438..225950251,2	MCF-7	breast:
8	chr1:225839340..225843768-chr1:225964006..225968066,9	MCF-7	breast:
9	chr1:225692749..225695160-chr1:225840876..225842568,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENAH	TF binding region
ENSG00000143742	Chromatin interaction
ENSG00000227496	Chromatin interaction
ENSG00000196187	Chromatin interaction
ENSG00000163041	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10082003	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12080606	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1360958	0.80[AMR][1000 genomes]
rs2035916	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs28818505	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3904084	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs475794	0.83[AMR][1000 genomes]
rs499385	0.80[AMR][1000 genomes]
rs525062	0.85[AMR][1000 genomes]
rs544404	0.85[AMR][1000 genomes]
rs544430	0.85[AMR][1000 genomes]
rs566085	0.85[AMR][1000 genomes]
rs59363938	0.83[AMR][1000 genomes]
rs9651009	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv3329174	chr1:225839754-225842702	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225837000-225842800	Active TSS	Psoas Muscle	Psoas
2	chr1:225837200-225842800	Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr1:225837600-225842400	Active TSS	H1 Cell Line	embryonic stem cell
4	chr1:225838000-225842400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr1:225838000-225842400	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr1:225838000-225842800	Active TSS	A549	lung
7	chr1:225838200-225842400	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr1:225838200-225842400	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:225838200-225842400	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr1:225838200-225842800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:225841400-225843000	Active TSS	Fetal Brain Male	brain
12	chr1:225841800-225842400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:225841800-225842400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:225841800-225842400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:225841800-225842400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:225841800-225842400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:225841800-225842400	Flanking Active TSS	Osteobl	bone
18	chr1:225841800-225842600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:225841800-225842600	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr1:225841800-225842800	Weak transcription	Small Intestine	intestine
21	chr1:225841800-225842800	Weak transcription	Stomach Mucosa	stomach
22	chr1:225841800-225843000	Enhancers	Hela-S3	cervix
23	chr1:225841800-225843200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr1:225841800-225843200	Flanking Active TSS	NHEK	skin
25	chr1:225841800-225844000	Enhancers	Fetal Heart	heart
26	chr1:225841800-225845000	Weak transcription	Lung	lung
27	chr1:225842000-225842400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:225842000-225842400	Flanking Active TSS	NH-A	brain
29	chr1:225842000-225842600	Weak transcription	Aorta	Aorta
30	chr1:225842000-225842800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:225842000-225842800	Weak transcription	Brain Germinal Matrix	brain
32	chr1:225842000-225842800	Weak transcription	Fetal Kidney	kidney
33	chr1:225842000-225842800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:225842000-225843600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:225842000-225843600	Enhancers	Brain Substantia Nigra	brain
36	chr1:225842000-225843800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr1:225842000-225844000	Enhancers	HepG2	liver
38	chr1:225842000-225844400	Enhancers	Rectal Smooth Muscle	rectum
39	chr1:225842000-225845000	Weak transcription	Left Ventricle	heart
40	chr1:225842000-225845200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:225842000-225845200	Weak transcription	Placenta	Placenta
42	chr1:225842000-225845200	Weak transcription	Ovary	ovary
43	chr1:225842000-225846000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:225842000-225865000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:225842200-225842400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr1:225842200-225842400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr1:225842200-225842400	Enhancers	Brain Angular Gyrus	brain
48	chr1:225842200-225842400	Weak transcription	NHLF	lung
49	chr1:225842200-225842600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:225842200-225842600	Enhancers	Brain Cingulate Gyrus	brain

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