Variant report

Variant	rs4233407
Chromosome Location	chr1:165652445-165652446
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:165639297..165642601-chr1:165650808..165654690,4	K562	blood:
2	chr1:165639297..165643636-chr1:165650808..165655625,4	K562	blood:
3	chr1:165651249..165652806-chr1:165666249..165668873,2	K562	blood:

Variant related genes	Relation type
ENSG00000143149	Chromatin interaction
ENSG00000215838	Chromatin interaction
ENSG00000230175	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10753687	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800129	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800130	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10800131	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918241	0.96[EUR][1000 genomes]
rs10918244	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1143659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807857	1.00[ASN][1000 genomes]
rs12565874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1538115	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1913844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1970286	0.85[EUR][1000 genomes]
rs2348734	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35247362	0.94[EUR][1000 genomes]
rs3738192	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3845537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41267568	1.00[ASN][1000 genomes]
rs41326750	1.00[ASN][1000 genomes]
rs4646881	1.00[ASN][1000 genomes]
rs4646886	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646887	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646888	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646889	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7368130	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519162	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543204	0.94[EUR][1000 genomes]
rs7546084	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555268	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4233407	ALDH9A1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165606200-165659600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:165619600-165653200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:165623400-165653000	Weak transcription	Stomach Mucosa	stomach
4	chr1:165629000-165653600	Strong transcription	Dnd41	blood
5	chr1:165629400-165652800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:165629400-165654200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:165629400-165656000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:165629600-165654800	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr1:165629800-165654800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:165630000-165654400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr1:165637800-165653400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:165638000-165666800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:165638600-165665400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:165639200-165659800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:165640000-165652800	Strong transcription	Fetal Intestine Large	intestine
16	chr1:165643000-165652600	Strong transcription	Fetal Thymus	thymus
17	chr1:165643400-165654800	Weak transcription	Right Atrium	heart
18	chr1:165644200-165652600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:165644400-165653400	Strong transcription	Fetal Muscle Trunk	muscle
20	chr1:165644600-165652600	Strong transcription	Fetal Lung	lung
21	chr1:165644600-165653400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:165644800-165653000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:165644800-165653400	Strong transcription	Placenta	Placenta
24	chr1:165644800-165658800	Strong transcription	HSMM	muscle
25	chr1:165645000-165655000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:165645000-165660200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:165645200-165652600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:165645200-165652800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:165645200-165653200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:165645200-165655200	Strong transcription	Primary B cells from cord blood	blood
31	chr1:165645600-165653000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:165645800-165655000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr1:165645800-165655400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:165645800-165657400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:165646000-165652800	Strong transcription	Fetal Stomach	stomach
36	chr1:165646000-165653400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:165646000-165655200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:165646200-165652600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr1:165646800-165654800	Weak transcription	Right Ventricle	heart
40	chr1:165647600-165652600	Strong transcription	Hela-S3	cervix
41	chr1:165647600-165652800	Strong transcription	NHDF-Ad	bronchial
42	chr1:165647600-165653800	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr1:165647800-165652800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:165647800-165658400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:165648000-165652600	Strong transcription	Brain Hippocampus Middle	brain
46	chr1:165648000-165652800	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr1:165648000-165652800	Strong transcription	Ovary	ovary
48	chr1:165648000-165653000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:165648200-165653400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:165648400-165652800	Strong transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links