Variant report

Variant	rs1045252
Chromosome Location	chr1:227181555-227181556
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1045285	0.81[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1045286	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[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];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1045287	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1045289	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1045290	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10495273	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916075	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11577007	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11578103	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11578479	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11580229	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11586604	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11587443	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11588904	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11589344	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12403236	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12406714	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12409230	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12409428	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12409755	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12410103	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12593	0.96[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1343743	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1343744	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17528667	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17592479	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17600627	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17600669	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17600725	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1929862	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1929863	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1929864	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2104860	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2183836	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297412	0.95[CEU][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2297415	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2297416	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2297418	0.87[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3738725	0.87[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3738729	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3768419	0.81[ASW][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3768421	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3768423	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3768424	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3768425	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3795445	0.81[ASW][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3795446	0.81[ASW][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3795449	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3795451	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3795453	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61834001	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61834004	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61834005	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61834006	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6426558	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6426559	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6659424	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6664955	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6670924	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6677602	0.92[CEU][hapmap]
rs6684821	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6690803	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6693535	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6699400	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6704144	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68087483	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7520272	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7535826	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7541033	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7549465	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7549586	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7552783	0.94[ASN][1000 genomes]
rs9726097	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9727512	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1045252	CABC1	cis	parietal	SCAN
rs1045252	ADCK3	cis	Whole Blood	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227158400-227183000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:227160800-227181800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:227162400-227181600	Weak transcription	NHEK	skin
5	chr1:227163400-227191200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:227173400-227183400	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:227174800-227182000	Weak transcription	NHDF-Ad	bronchial
8	chr1:227175200-227198400	Weak transcription	A549	lung
9	chr1:227175200-227210200	Weak transcription	HMEC	breast
10	chr1:227175400-227182600	Genic enhancers	Fetal Intestine Small	intestine
11	chr1:227175600-227181600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:227175600-227182200	Weak transcription	Brain Germinal Matrix	brain
13	chr1:227175600-227183200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:227175600-227216200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:227175800-227181800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:227175800-227181800	Enhancers	Fetal Intestine Large	intestine
17	chr1:227176000-227181800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:227176000-227181800	Strong transcription	Fetal Muscle Trunk	muscle
19	chr1:227176000-227190200	Weak transcription	Esophagus	oesophagus
20	chr1:227176000-227191800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:227176000-227216400	Weak transcription	NHLF	lung
22	chr1:227176200-227181800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:227176400-227190400	Weak transcription	Osteobl	bone
24	chr1:227176600-227181800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:227176600-227182400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:227176600-227190000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:227177000-227181600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:227177000-227181600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:227177000-227181800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:227177000-227181800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:227177200-227181800	Weak transcription	Aorta	Aorta
32	chr1:227177200-227181800	Weak transcription	Gastric	stomach
33	chr1:227177200-227188600	Weak transcription	Fetal Lung	lung
34	chr1:227177400-227181800	Weak transcription	Brain Angular Gyrus	brain
35	chr1:227177400-227255200	Weak transcription	Small Intestine	intestine
36	chr1:227177600-227181600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:227177600-227181600	Weak transcription	Fetal Brain Female	brain
38	chr1:227178000-227183200	Strong transcription	Fetal Stomach	stomach
39	chr1:227178200-227183000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:227178200-227188600	Weak transcription	HSMMtube	muscle
41	chr1:227178400-227181600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:227178400-227181800	Weak transcription	Colonic Mucosa	Colon
43	chr1:227178400-227181800	Weak transcription	Left Ventricle	heart
44	chr1:227178400-227181800	Weak transcription	Lung	lung
45	chr1:227178400-227181800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:227178400-227182200	Weak transcription	Brain Anterior Caudate	brain
47	chr1:227178400-227190400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:227178400-227271200	Weak transcription	Psoas Muscle	Psoas
49	chr1:227178600-227181600	Weak transcription	Colon Smooth Muscle	Colon
50	chr1:227178600-227181800	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links