Variant report

Variant	rs9430123
Chromosome Location	chr1:213443639-213443640
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10127851	0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10864034	0.84[AMR][1000 genomes]
rs10864036	0.83[AMR][1000 genomes]
rs10864038	0.94[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1391549	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1391550	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1498357	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1566247	0.84[AMR][1000 genomes]
rs17020338	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1995151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2173398	0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2494767	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2647387	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2817976	0.98[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2817978	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2817981	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2817984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2841425	0.85[ASN][1000 genomes]
rs2841427	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2841439	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4655386	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4951479	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs4951677	0.95[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6419469	0.90[AMR][1000 genomes]
rs6419470	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6540778	0.83[AMR][1000 genomes]
rs6540780	0.86[AMR][1000 genomes]
rs6540781	0.91[AMR][1000 genomes]
rs6540782	0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6657234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes]
rs6658259	0.82[AMR][1000 genomes]
rs6666814	0.83[AMR][1000 genomes]
rs6671872	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs6691488	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs6692056	0.86[AMR][1000 genomes]
rs6692144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes]
rs6693291	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6697921	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs6700169	0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7535369	0.94[AMR][1000 genomes]
rs7547274	0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9308430	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9429901	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9429902	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9430118	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9430120	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9430121	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9430122	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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	esv3392967	chr1:213271844-213490132	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9430123	BATF3	cis	parietal	SCAN
rs9430123	ANGEL2	cis	parietal	SCAN
rs9430123	ANGEL2	cis	cerebellum	SCAN
rs9430123	KCNH1	cis	cerebellum	SCAN
rs9430123	ANGEL2	cis	Esophagus Mucosa	GTEx
rs9430123	RPS6KC1	cis	Artery Tibial	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213388200-213455400	Weak transcription	Placenta	Placenta
2	chr1:213401200-213447400	Weak transcription	Small Intestine	intestine
3	chr1:213402800-213454800	Weak transcription	Brain Substantia Nigra	brain
4	chr1:213405600-213454800	Weak transcription	Brain Angular Gyrus	brain
5	chr1:213405800-213457600	Weak transcription	NHLF	lung
6	chr1:213406000-213450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:213406200-213445600	Weak transcription	NHDF-Ad	bronchial
8	chr1:213406200-213454800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:213412600-213452400	Weak transcription	Right Ventricle	heart
10	chr1:213414800-213445400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:213414800-213445600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:213415400-213450200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr1:213415600-213447200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:213415600-213451000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:213415600-213453800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:213417200-213453600	Weak transcription	HSMMtube	muscle
17	chr1:213418400-213449200	Weak transcription	Fetal Lung	lung
18	chr1:213425000-213447400	Weak transcription	Pancreas	Pancrea
19	chr1:213425400-213444200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:213427000-213446200	Weak transcription	A549	lung
21	chr1:213427000-213451400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr1:213431200-213450600	Weak transcription	Psoas Muscle	Psoas
23	chr1:213433800-213454800	Weak transcription	Brain Anterior Caudate	brain
24	chr1:213434400-213454800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:213434400-213454800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:213434600-213449200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:213434600-213453800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:213434600-213453800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:213435000-213445600	Weak transcription	K562	blood
30	chr1:213435000-213445800	Weak transcription	Liver	Liver
31	chr1:213435200-213456200	Weak transcription	Esophagus	oesophagus
32	chr1:213436400-213447600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:213438600-213445600	Weak transcription	Osteobl	bone
34	chr1:213438600-213449600	Weak transcription	Gastric	stomach
35	chr1:213440000-213447000	Weak transcription	Primary B cells from cord blood	blood
36	chr1:213440000-213451400	Weak transcription	NH-A	brain
37	chr1:213440000-213469800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:213440400-213450800	Weak transcription	Fetal Stomach	stomach
39	chr1:213440600-213445400	Weak transcription	Adipose Nuclei	Adipose
40	chr1:213440600-213447200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:213440600-213449400	Weak transcription	Ovary	ovary
42	chr1:213440600-213449800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr1:213440600-213452400	Weak transcription	Aorta	Aorta
44	chr1:213440600-213454200	Weak transcription	Fetal Muscle Leg	muscle
45	chr1:213440600-213454400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:213440600-213454800	Weak transcription	Left Ventricle	heart
47	chr1:213440800-213445600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:213440800-213447200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:213440800-213447400	Weak transcription	Primary T cells from cord blood	blood
50	chr1:213440800-213447400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links