Variant report

Variant	rs1269729
Chromosome Location	chr1:95390438-95390439
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr1:95390400-95392702	H1-hESC	embryonic stem cell:	n/a	n/a
2	MXI1	chr1:95390217-95393728	IMR90	lung:	n/a	chr1:95393426-95393435 chr1:95393424-95393433
3	POLR2A	chr1:95390227-95394539	HepG2	liver:	n/a	n/a
4	MXI1	chr1:95390079-95394077	SK-N-SH	brain:	n/a	chr1:95393426-95393435 chr1:95393424-95393433
5	POLR2A	chr1:95390209-95392231	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr1:95389178-95394521	H1-hESC	embryonic stem cell:	n/a	n/a
7	REST	chr1:95390272-95393707	H1-neurons	neurons:	n/a	chr1:95391947-95391957 chr1:95393046-95393059 chr1:95392474-95392481 chr1:95391793-95391811 chr1:95391945-95391959
8	CHD1	chr1:95390093-95394059	IMR90	lung:	n/a	chr1:95392766-95392776
9	NFIC	chr1:95390364-95393119	SK-N-SH	brain:	n/a	n/a
10	FOS	chr1:95390424-95390523	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
CNN3	TF binding region
ENSG00000235501	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1146466	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1146468	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1265173	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1265174	1.00[EUR][1000 genomes]
rs1832961	1.00[EUR][1000 genomes]
rs2766009	1.00[EUR][1000 genomes]
rs2797627	1.00[EUR][1000 genomes]
rs4083970	1.00[EUR][1000 genomes]
rs56785527	1.00[EUR][1000 genomes]
rs6691935	1.00[EUR][1000 genomes]
rs698970	1.00[EUR][1000 genomes]
rs72964574	1.00[EUR][1000 genomes]
rs72964575	1.00[EUR][1000 genomes]
rs7543891	1.00[EUR][1000 genomes]
rs859049	1.00[EUR][1000 genomes]
rs859056	1.00[EUR][1000 genomes]
rs859059	1.00[EUR][1000 genomes]
rs859083	1.00[EUR][1000 genomes]
rs943200	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv947291	chr1:95382933-95393244	Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95357800-95390800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:95368400-95390600	Weak transcription	Fetal Thymus	thymus
3	chr1:95385600-95390600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:95386400-95390600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:95386600-95391000	Transcr. at gene 5' and 3'	HSMM	muscle
6	chr1:95387000-95395400	Active TSS	Aorta	Aorta
7	chr1:95388200-95390600	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr1:95388400-95391200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:95388400-95393600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:95389000-95390600	Weak transcription	Placenta	Placenta
11	chr1:95389200-95390600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:95389200-95390600	Weak transcription	Stomach Mucosa	stomach
13	chr1:95389400-95390800	Flanking Active TSS	Liver	Liver
14	chr1:95389400-95391000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:95389400-95391000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
16	chr1:95389400-95391600	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr1:95389600-95390600	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr1:95389600-95391200	Active TSS	Psoas Muscle	Psoas
19	chr1:95389600-95393400	Active TSS	Brain Anterior Caudate	brain
20	chr1:95389600-95393600	Active TSS	Brain Substantia Nigra	brain
21	chr1:95389600-95393600	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr1:95389600-95395000	Active TSS	Ovary	ovary
23	chr1:95389600-95395000	Active TSS	Right Atrium	heart
24	chr1:95389800-95390600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:95389800-95390800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:95389800-95390800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:95389800-95390800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:95389800-95391000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:95389800-95391000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
30	chr1:95389800-95391200	Flanking Active TSS	HUVEC	blood vessel
31	chr1:95389800-95393000	Active TSS	NH-A	brain
32	chr1:95389800-95393600	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr1:95389800-95393600	Active TSS	NHLF	lung
34	chr1:95389800-95395200	Active TSS	HSMMtube	muscle
35	chr1:95390000-95390600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:95390000-95390600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:95390000-95390600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:95390000-95390600	Active TSS	Brain Angular Gyrus	brain
39	chr1:95390000-95390600	Weak transcription	Pancreas	Pancrea
40	chr1:95390000-95390600	Flanking Active TSS	HepG2	liver
41	chr1:95390000-95391000	Weak transcription	Gastric	stomach
42	chr1:95390000-95392200	Active TSS	Colonic Mucosa	Colon
43	chr1:95390000-95393200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:95390000-95393200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:95390000-95393200	Active TSS	Muscle Satellite Cultured Cells	--
46	chr1:95390000-95393200	Active TSS	NHDF-Ad	bronchial
47	chr1:95390000-95393400	Active TSS	HMEC	breast
48	chr1:95390000-95393600	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr1:95390000-95393600	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr1:95390000-95393600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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