Variant report

Variant	rs3753658
Chromosome Location	chr1:226012686-226012687
allele	G/T
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	POLR2A	chr1:226011974-226013818	A549	lung:	n/a	n/a
2	POLR2A	chr1:226012634-226013154	HepG2	liver:	n/a	n/a
3	MAX	chr1:226012633-226013298	HepG2	liver:	n/a	n/a
4	MYBL2	chr1:226012653-226013165	HepG2	liver:	n/a	n/a
5	FOXA1	chr1:226012668-226013108	HepG2	liver:	n/a	n/a
6	MAX	chr1:226012642-226013579	HepG2	liver:	n/a	n/a
7	HNF4G	chr1:226012653-226013155	HepG2	liver:	n/a	chr1:226012935-226012943 chr1:226012925-226012940 chr1:226012836-226012848
8	HDAC2	chr1:226012677-226013177	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:226012407-226012762	H1-neurons	neurons:	n/a	n/a
10	GATA1	chr1:226012614-226013324	PBDE	blood:	n/a	n/a
11	POLR2A	chr1:226012393-226012756	H1-neurons	neurons:	n/a	n/a
12	HDAC2	chr1:226012682-226013228	HepG2	liver:	n/a	n/a
13	FOXA1	chr1:226012676-226013147	HepG2	liver:	n/a	n/a
14	EP300	chr1:226012652-226013199	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
EPHX1	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11587295	1.00[AFR][1000 genomes]
rs11587753	1.00[AFR][1000 genomes]
rs11588167	1.00[AFR][1000 genomes]
rs11588197	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs11588766	1.00[AFR][1000 genomes]
rs12568108	1.00[ASW][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes]
rs3738035	0.80[CHB][hapmap]
rs3738045	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3753659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149222	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs45607741	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56187333	1.00[AFR][1000 genomes]
rs61837988	1.00[AFR][1000 genomes]
rs61837989	1.00[AFR][1000 genomes]
rs61837991	1.00[AFR][1000 genomes]
rs61837993	1.00[AFR][1000 genomes]
rs61837995	1.00[AFR][1000 genomes]
rs61837996	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv947519	chr1:225998770-226034631	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3753658	HLX	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226000000-226019400	Weak transcription	Fetal Brain Female	brain
2	chr1:226000400-226015800	Enhancers	Ovary	ovary
3	chr1:226001800-226019200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:226005600-226019400	Weak transcription	Brain Germinal Matrix	brain
5	chr1:226005800-226013000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:226005800-226013400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:226005800-226019200	Weak transcription	NHLF	lung
8	chr1:226005800-226019400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:226005800-226019400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr1:226006200-226013200	Weak transcription	HSMMtube	muscle
11	chr1:226006200-226013600	Weak transcription	Small Intestine	intestine
12	chr1:226006200-226016600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:226006200-226019400	Weak transcription	HSMM	muscle
14	chr1:226006200-226022000	Weak transcription	NHDF-Ad	bronchial
15	chr1:226006400-226013000	Weak transcription	Osteobl	bone
16	chr1:226006400-226014200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:226006400-226014800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr1:226006400-226016800	Weak transcription	Colonic Mucosa	Colon
19	chr1:226006400-226018600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:226006400-226019400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:226006400-226019600	Weak transcription	Hela-S3	cervix
22	chr1:226006600-226016600	Weak transcription	Aorta	Aorta
23	chr1:226008600-226013200	Weak transcription	Fetal Kidney	kidney
24	chr1:226008800-226013400	Weak transcription	HMEC	breast
25	chr1:226008800-226019400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:226009400-226013400	Genic enhancers	Fetal Lung	lung
27	chr1:226009800-226015400	Enhancers	Colon Smooth Muscle	Colon
28	chr1:226010000-226012800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr1:226010200-226013600	Enhancers	Brain Substantia Nigra	brain
30	chr1:226010400-226015000	Enhancers	Gastric	stomach
31	chr1:226010800-226013000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:226010800-226013000	Weak transcription	Esophagus	oesophagus
33	chr1:226010800-226015400	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr1:226010800-226016600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:226010800-226019200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:226011000-226013600	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr1:226011000-226013800	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr1:226011000-226014600	Enhancers	Right Atrium	heart
39	chr1:226011000-226015200	Enhancers	Brain Hippocampus Middle	brain
40	chr1:226011000-226015800	Enhancers	Fetal Muscle Trunk	muscle
41	chr1:226011000-226015800	Genic enhancers	Fetal Muscle Leg	muscle
42	chr1:226011000-226016800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:226011200-226013000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:226011200-226013000	Weak transcription	A549	lung
45	chr1:226011200-226013200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:226011200-226013600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:226011200-226013800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:226011200-226014000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:226011200-226014400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:226011200-226015000	Enhancers	Right Ventricle	heart

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