Variant report

Variant	rs10429871
Chromosome Location	chr1:225842491-225842492
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 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	chr1:225840526-225842504	U87	brain:	n/a	n/a
4	POLR2A	chr1:225840532-225842504	U87	brain:	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
ENSG00000227496	Chromatin interaction
ENSG00000143742	Chromatin interaction
ENSG00000196187	Chromatin interaction
ENSG00000163041	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11801322	0.86[EUR][1000 genomes]
rs12027872	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12033453	0.96[ASN][1000 genomes]
rs12038461	0.86[ASN][1000 genomes]
rs12038893	0.90[ASN][1000 genomes]
rs12039453	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16845153	0.82[ASN][1000 genomes]
rs17502774	0.82[EUR][1000 genomes]
rs17502823	0.88[EUR][1000 genomes]
rs17502858	0.88[EUR][1000 genomes]
rs17502961	0.88[EUR][1000 genomes]
rs17503792	0.93[EUR][1000 genomes]
rs17561781	0.82[EUR][1000 genomes]
rs17562010	0.88[EUR][1000 genomes]
rs17562052	0.88[EUR][1000 genomes]
rs17568665	0.88[EUR][1000 genomes]
rs17569049	0.93[EUR][1000 genomes]
rs17569145	0.93[EUR][1000 genomes]
rs1870834	0.85[ASN][1000 genomes]
rs28617210	0.90[EUR][1000 genomes]
rs56793390	0.93[ASN][1000 genomes]
rs6687755	0.86[EUR][1000 genomes]
rs73125707	0.88[EUR][1000 genomes]
rs74147627	0.85[ASN][1000 genomes]
rs954615	0.88[EUR][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:80 , 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	chr1:225838000-225842800	Active TSS	A549	lung
4	chr1:225838200-225842800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:225841400-225843000	Active TSS	Fetal Brain Male	brain
6	chr1:225841800-225842600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:225841800-225842600	Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr1:225841800-225842800	Weak transcription	Small Intestine	intestine
9	chr1:225841800-225842800	Weak transcription	Stomach Mucosa	stomach
10	chr1:225841800-225843000	Enhancers	Hela-S3	cervix
11	chr1:225841800-225843200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr1:225841800-225843200	Flanking Active TSS	NHEK	skin
13	chr1:225841800-225844000	Enhancers	Fetal Heart	heart
14	chr1:225841800-225845000	Weak transcription	Lung	lung
15	chr1:225842000-225842600	Weak transcription	Aorta	Aorta
16	chr1:225842000-225842800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:225842000-225842800	Weak transcription	Brain Germinal Matrix	brain
18	chr1:225842000-225842800	Weak transcription	Fetal Kidney	kidney
19	chr1:225842000-225842800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:225842000-225843600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:225842000-225843600	Enhancers	Brain Substantia Nigra	brain
22	chr1:225842000-225843800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr1:225842000-225844000	Enhancers	HepG2	liver
24	chr1:225842000-225844400	Enhancers	Rectal Smooth Muscle	rectum
25	chr1:225842000-225845000	Weak transcription	Left Ventricle	heart
26	chr1:225842000-225845200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:225842000-225845200	Weak transcription	Placenta	Placenta
28	chr1:225842000-225845200	Weak transcription	Ovary	ovary
29	chr1:225842000-225846000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:225842000-225865000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:225842200-225842600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:225842200-225842600	Enhancers	Brain Cingulate Gyrus	brain
33	chr1:225842200-225842600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:225842200-225842600	Enhancers	Right Atrium	heart
35	chr1:225842200-225842800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr1:225842200-225842800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:225842200-225842800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:225842200-225842800	Weak transcription	Brain Anterior Caudate	brain
39	chr1:225842200-225842800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:225842200-225842800	Weak transcription	Fetal Intestine Large	intestine
41	chr1:225842200-225842800	Enhancers	Fetal Muscle Trunk	muscle
42	chr1:225842200-225842800	Weak transcription	HSMM	muscle
43	chr1:225842200-225842800	Enhancers	NHDF-Ad	bronchial
44	chr1:225842200-225843000	Enhancers	Fetal Lung	lung
45	chr1:225842200-225843000	Enhancers	Stomach Smooth Muscle	stomach
46	chr1:225842200-225843200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:225842200-225843200	Enhancers	Brain Hippocampus Middle	brain
48	chr1:225842200-225843200	Weak transcription	Fetal Brain Female	brain
49	chr1:225842200-225843400	Enhancers	HUVEC	blood vessel
50	chr1:225842200-225844000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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