Variant report

Variant	rs7546084
Chromosome Location	chr1:165655816-165655817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:165654992..165657269-chr1:165796152..165797744,2	MCF-7	breast:
2	chr1:165570621..165571411-chr1:165655068..165656040,3	MCF-7	breast:
3	chr1:165654373..165656083-chr1:165811609..165814179,2	K562	blood:

Variant related genes	Relation type
ENSG00000143179	Chromatin interaction
ENSG00000143183	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10753687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800128	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800129	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800130	0.93[EUR][1000 genomes]
rs10800131	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918241	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10918244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1143659	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807857	1.00[ASN][1000 genomes]
rs12565874	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337442	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337443	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1538115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1913844	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1970286	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2348734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882006	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35247362	0.88[EUR][1000 genomes]
rs3738192	0.93[EUR][1000 genomes]
rs3845537	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41267568	1.00[ASN][1000 genomes]
rs41326750	1.00[ASN][1000 genomes]
rs4233407	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646881	1.00[ASN][1000 genomes]
rs4646886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646887	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646888	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646889	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4646891	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656457	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657462	0.85[AFR][1000 genomes]
rs7368130	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543204	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7555268	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555787	0.82[AMR][1000 genomes];0.94[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
rs7546084	ALDH9A1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:121 , 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	chr1:165629400-165656000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:165638000-165666800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:165638600-165665400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:165639200-165659800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:165644800-165658800	Strong transcription	HSMM	muscle
7	chr1:165645000-165660200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:165645800-165657400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:165647800-165658400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:165650000-165666800	Weak transcription	Colonic Mucosa	Colon
11	chr1:165651600-165659600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:165651600-165665400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:165651600-165667200	Weak transcription	Gastric	stomach
14	chr1:165651800-165665200	Weak transcription	Brain Substantia Nigra	brain
15	chr1:165651800-165665200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:165651800-165665400	Weak transcription	Small Intestine	intestine
17	chr1:165652000-165664000	Weak transcription	Fetal Brain Male	brain
18	chr1:165652200-165656000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:165652200-165657000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:165652200-165657400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr1:165652200-165665400	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:165652200-165665800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:165652200-165666000	Weak transcription	Fetal Kidney	kidney
24	chr1:165652200-165666800	Weak transcription	Lung	lung
25	chr1:165652400-165656400	Weak transcription	Fetal Brain Female	brain
26	chr1:165652400-165657200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:165652400-165657200	Weak transcription	HepG2	liver
28	chr1:165652400-165657400	Weak transcription	HUVEC	blood vessel
29	chr1:165652400-165658800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:165652400-165659200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:165652400-165659400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:165652400-165659600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:165652400-165659600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:165652400-165659600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:165652400-165659600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:165652400-165659800	Weak transcription	Brain Angular Gyrus	brain
37	chr1:165652400-165665200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr1:165652400-165665400	Weak transcription	HMEC	breast
39	chr1:165652400-165665400	Weak transcription	NH-A	brain
40	chr1:165652400-165665800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:165652400-165665800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:165652400-165665800	Weak transcription	HSMMtube	muscle
43	chr1:165652400-165666800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr1:165652400-165666800	Weak transcription	Esophagus	oesophagus
45	chr1:165652400-165667000	Weak transcription	Pancreas	Pancrea
46	chr1:165652400-165667000	Weak transcription	Spleen	Spleen
47	chr1:165652600-165656000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr1:165652600-165657600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr1:165652600-165666000	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:165652800-165656400	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links