Variant report

Variant	rs1418150
Chromosome Location	chr1:223438771-223438772
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223438407..223440755-chr1:223638365..223640039,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10495206	0.82[JPT][hapmap]
rs11486078	0.93[ASN][1000 genomes]
rs1341988	0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs1400959	0.82[JPT][hapmap]
rs1400961	0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs1400963	0.91[ASW][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.83[AFR][1000 genomes]
rs1418152	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[TSI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1418153	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1640846	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1640849	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17161988	0.83[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs17163765	0.85[CEU][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17479856	1.00[ASW][hapmap];0.85[CEU][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17480087	0.82[JPT][hapmap]
rs17517952	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17518077	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17518349	0.82[JPT][hapmap]
rs17518363	0.82[JPT][hapmap]
rs17538964	1.00[ASW][hapmap];0.85[CEU][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17539269	0.82[JPT][hapmap]
rs17576822	0.85[CEU][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17577025	1.00[ASW][hapmap];0.85[CEU][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17577212	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1773710	0.92[EUR][1000 genomes]
rs1773713	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1829310	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28561511	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3820596	0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs61837626	0.93[ASN][1000 genomes]
rs61837627	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61837629	0.87[EUR][1000 genomes]
rs61837630	0.87[EUR][1000 genomes]
rs61837633	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61837634	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61837635	0.83[EUR][1000 genomes]
rs61837638	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61837640	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61838191	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61838192	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61838194	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61838197	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61838199	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs712857	0.81[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs712858	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73122234	0.83[EUR][1000 genomes]
rs7412060	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs74145795	0.87[EUR][1000 genomes]
rs7518292	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs851194	0.85[EUR][1000 genomes]
rs851196	0.82[EUR][1000 genomes]
rs885279	0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs9442040	0.90[EUR][1000 genomes]
rs9442043	0.91[AFR][1000 genomes];0.95[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	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1000039	chr1:223429733-223527845	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1418150	SUSD4	cis	multi-tissue	Pritchard
rs1418150	SUSD4	cis	parietal	SCAN
rs1418150	SUSD4	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223423800-223439600	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr1:223424200-223438800	Weak transcription	Ovary	ovary
3	chr1:223427400-223442000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr1:223432200-223440200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:223432400-223442200	Weak transcription	Pancreas	Pancrea
6	chr1:223432600-223438800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:223433200-223444600	Weak transcription	Esophagus	oesophagus
8	chr1:223433600-223440400	Weak transcription	Fetal Intestine Large	intestine
9	chr1:223437000-223438800	Enhancers	K562	blood
10	chr1:223437400-223439200	Strong transcription	Primary T cells from cord blood	blood
11	chr1:223438000-223443600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:223438200-223438800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr1:223438200-223439000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:223438400-223439200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:223438400-223440400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:223438400-223441000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:223438600-223438800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:223438600-223442800	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links