Variant report

Variant	rs885279
Chromosome Location	chr1:223442673-223442674
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223439513..223441100-chr1:223441175..223442688,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1341291	0.93[YRI][hapmap]
rs1400961	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1418150	0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs1418152	0.84[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs1418153	0.91[EUR][1000 genomes]
rs1640846	0.80[EUR][1000 genomes]
rs1640849	0.94[ASW][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs17161988	1.00[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17163762	0.92[LWK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes]
rs17163765	0.94[ASW][hapmap];0.84[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs17163773	0.93[YRI][hapmap]
rs17163774	0.93[YRI][hapmap]
rs17163825	0.81[JPT][hapmap]
rs17479856	0.84[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs17487717	0.85[YRI][hapmap]
rs17517952	0.89[EUR][1000 genomes]
rs17518077	0.89[EUR][1000 genomes]
rs17538964	0.84[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs17576822	0.84[CEU][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs17577025	0.84[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs17577212	0.89[EUR][1000 genomes]
rs1773710	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1773713	0.80[EUR][1000 genomes]
rs1829310	0.88[EUR][1000 genomes]
rs1949441	0.85[YRI][hapmap]
rs2176505	0.82[YRI][hapmap]
rs2203763	0.93[YRI][hapmap]
rs28561511	0.88[EUR][1000 genomes]
rs34468460	0.82[YRI][hapmap]
rs3820596	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61837629	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61837630	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61837633	0.93[EUR][1000 genomes]
rs61837634	0.91[EUR][1000 genomes]
rs61837635	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61837636	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61837638	0.91[EUR][1000 genomes]
rs61837640	0.91[EUR][1000 genomes]
rs61838191	0.90[EUR][1000 genomes]
rs61838192	0.90[EUR][1000 genomes]
rs61838194	0.90[EUR][1000 genomes]
rs61838197	0.88[EUR][1000 genomes]
rs61838199	0.88[EUR][1000 genomes]
rs712857	0.88[ASW][hapmap];0.81[CEU][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73122234	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7412060	0.90[EUR][1000 genomes]
rs74145795	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7518292	0.90[EUR][1000 genomes]
rs7536652	0.90[JPT][hapmap]
rs851194	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs851196	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs851201	0.87[CHD][hapmap];0.95[JPT][hapmap]
rs9442040	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9442043	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs885279	SUSD4	cis	parietal	SCAN
rs885279	SUSD4	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223433200-223444600	Weak transcription	Esophagus	oesophagus
2	chr1:223438000-223443600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:223438600-223442800	Weak transcription	Gastric	stomach
4	chr1:223440400-223446000	Weak transcription	Brain Anterior Caudate	brain
5	chr1:223440800-223465600	Weak transcription	Ovary	ovary
6	chr1:223441200-223445600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:223442000-223443400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:223442000-223444000	Enhancers	Fetal Heart	heart
9	chr1:223442200-223442800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:223442200-223443000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr1:223442200-223443000	Enhancers	Pancreas	Pancrea
12	chr1:223442200-223443000	Enhancers	K562	blood
13	chr1:223442200-223445400	Enhancers	Liver	Liver
14	chr1:223442400-223443000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:223442400-223443000	Enhancers	Fetal Intestine Small	intestine
16	chr1:223442400-223443000	Enhancers	HepG2	liver
17	chr1:223442400-223443400	Enhancers	Fetal Intestine Large	intestine
18	chr1:223442400-223443800	Enhancers	Stomach Mucosa	stomach
19	chr1:223442600-223462200	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links