Variant report

Variant	rs4657468
Chromosome Location	chr1:165668293-165668294
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:165667396-165668306	U87	brain:	n/a	n/a
2	MTA3	chr1:165667866-165668315	GM12878	blood:	n/a	n/a
3	E2F6	chr1:165667280-165668330	A549	lung:	n/a	n/a
4	POLR2A	chr1:165667341-165668299	SK-N-SH	brain:	n/a	n/a
5	REST	chr1:165667269-165668304	A549	lung:	n/a	n/a
6	MXI1	chr1:165666649-165668519	SK-N-SH	brain:	n/a	n/a
7	GTF2F1	chr1:165667191-165668338	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:165667335-165668306	U87	brain:	n/a	n/a
9	REST	chr1:165667150-165668332	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr1:165667257-165668295	HUVEC	blood vessel:	n/a	n/a
11	RFX5	chr1:165667183-165668294	Hela-S3	cervix:	n/a	n/a
12	RUNX3	chr1:165667051-165668366	GM12878	blood:	n/a	n/a
13	MAX	chr1:165667328-165668294	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:165667107-165668369	H1-hESC	embryonic stem cell:	n/a	n/a
15	PML	chr1:165667194-165668308	GM12878	blood:	n/a	n/a
16	RUNX3	chr1:165667284-165668334	GM12878	blood:	n/a	n/a
17	GTF2F1	chr1:165668132-165668298	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr1:165667123-165668312	GM12892	blood:	n/a	n/a
19	POLR2A	chr1:165667144-165668325	SK-N-MC	brain:	n/a	n/a
20	MYC	chr1:165667274-165668293	NB4	blood:	n/a	n/a
21	POLR2A	chr1:165666817-165668369	Hela-S3	cervix:	n/a	n/a
22	MAZ	chr1:165667276-165668299	GM12878	blood:	n/a	n/a
23	TCF12	chr1:165666748-165668424	A549	lung:	n/a	n/a
24	MAX	chr1:165667085-165668342	A549	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:165668238..165670395-chr1:165671398..165673418,3	K562	blood:
2	chr1:165666837..165669027-chr1:165796687..165798880,2	MCF-7	breast:
3	chr1:165599643..165601355-chr1:165666069..165669053,3	MCF-7	breast:
4	chr1:165667536..165669486-chr1:165736821..165739691,4	MCF-7	breast:
5	chr1:165599737..165602284-chr1:165666440..165669733,4	K562	blood:
6	chr1:165666145..165668955-chr1:165675306..165678474,3	K562	blood:
7	chr1:165666281..165669188-chr1:165795955..165797975,3	MCF-7	breast:
8	chr1:165600029..165602046-chr1:165667210..165669353,5	K562	blood:

No data

Variant related genes	Relation type
ALDH9A1	TF binding region
ENSG00000143183	Chromatin interaction
ENSG00000224358	Chromatin interaction
ENSG00000143198	Chromatin interaction
ENSG00000215838	Chromatin interaction
ENSG00000143179	Chromatin interaction
ENSG00000273365	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10753688	0.80[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs10800132	0.83[ASN][1000 genomes]
rs10918242	0.86[ASN][1000 genomes]
rs10918251	0.83[ASN][1000 genomes]
rs10918252	0.84[ASN][1000 genomes]
rs12033254	0.83[CHD][hapmap];0.84[JPT][hapmap]
rs12036561	0.86[ASN][1000 genomes]
rs12037790	0.83[ASN][1000 genomes]
rs12084748	0.83[ASN][1000 genomes]
rs12409168	0.83[ASN][1000 genomes]
rs12567331	0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12728137	0.84[ASN][1000 genomes]
rs17482717	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4307543	0.86[ASN][1000 genomes]
rs4646883	0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4646885	0.82[ASN][1000 genomes]
rs4657463	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4657466	0.83[ASN][1000 genomes]
rs71628390	0.83[ASN][1000 genomes]
rs7541817	0.86[ASN][1000 genomes]
rs7546322	0.83[ASN][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	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4657468	ALDH9A1	cis	Esophagus Muscularis	GTEx
rs4657468	ALDH9A1	cis	cerebellum	SCAN
rs4657468	ALDH9A1	Cis_1M	lymphoblastoid	RTeQTL
rs4657468	ALDH9A1	cis	parietal	SCAN
rs4657468	ALDH9A1	cis	lymphoblastoid	seeQTL
rs4657468	MGST3	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165665400-165668400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:165665400-165668400	Active TSS	NHLF	lung
3	chr1:165665800-165668400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:165665800-165668400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:165665800-165668400	Active TSS	Fetal Brain Female	brain
6	chr1:165666000-165668400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:165666000-165668400	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr1:165666000-165668400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:165666000-165668400	Active TSS	Right Atrium	heart
10	chr1:165666200-165668400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:165666200-165668400	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr1:165666200-165668400	Active TSS	Stomach Smooth Muscle	stomach
13	chr1:165666200-165668400	Active TSS	A549	lung
14	chr1:165666400-165668400	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr1:165666400-165668400	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr1:165666400-165668400	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr1:165666400-165668400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:165666400-165668400	Active TSS	Rectal Smooth Muscle	rectum
19	chr1:165666400-165668600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:165666600-165668400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:165666600-165668400	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr1:165666600-165668400	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr1:165666600-165668400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:165666600-165668400	Active TSS	Brain Cingulate Gyrus	brain
25	chr1:165666600-165668400	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr1:165666600-165668400	Active TSS	Fetal Intestine Small	intestine
27	chr1:165666600-165668400	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr1:165666600-165668400	Active TSS	GM12878-XiMat	blood
29	chr1:165666600-165668400	Active TSS	HSMM	muscle
30	chr1:165666600-165668400	Active TSS	HSMMtube	muscle
31	chr1:165666600-165668400	Active TSS	NHDF-Ad	bronchial
32	chr1:165666800-165668400	Active TSS	H1 Cell Line	embryonic stem cell
33	chr1:165666800-165668400	Active TSS	H9 Cell Line	embryonic stem cell
34	chr1:165666800-165668400	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr1:165666800-165668400	Active TSS	Brain Anterior Caudate	brain
36	chr1:165666800-165668400	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr1:165666800-165668400	Active TSS	Fetal Kidney	kidney
38	chr1:165666800-165668400	Active TSS	Right Ventricle	heart
39	chr1:165666800-165668400	Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr1:165667000-165668400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:165667000-165668400	Active TSS	Primary T cells from cord blood	blood
42	chr1:165667000-165668400	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr1:165667000-165668400	Active TSS	Muscle Satellite Cultured Cells	--
44	chr1:165667000-165668400	Active TSS	Brain Hippocampus Middle	brain
45	chr1:165667000-165668400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:165667000-165668400	Active TSS	Brain Substantia Nigra	brain
47	chr1:165667000-165668400	Active TSS	Duodenum Mucosa	Duodenum
48	chr1:165667000-165668400	Active TSS	Fetal Brain Male	brain
49	chr1:165667000-165668400	Active TSS	Fetal Intestine Large	intestine
50	chr1:165667000-165668400	Active TSS	Pancreatic Islets	Pancreatic Islet

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