Variant report

Variant	rs9288025
Chromosome Location	chr2:180088516-180088517
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	chr2:180084814..180086461-chr2:180088409..180090009,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10084229	0.89[JPT][hapmap]
rs10164707	0.94[CEU][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs10164814	0.89[CEU][hapmap];0.88[JPT][hapmap]
rs10173710	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10181464	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs10188759	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs10194534	0.87[ASN][1000 genomes]
rs10196577	0.96[AFR][1000 genomes]
rs10208593	0.89[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes]
rs10209887	0.83[CEU][hapmap]
rs10930855	0.89[JPT][hapmap]
rs10930857	0.86[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes]
rs10930859	0.87[ASN][1000 genomes]
rs1159257	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs12621023	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12621115	0.94[CEU][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs12622075	0.83[CEU][hapmap]
rs12693175	0.89[JPT][hapmap]
rs12693179	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs12987285	0.94[CEU][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs13029576	0.88[JPT][hapmap]
rs13382185	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs13396334	0.89[JPT][hapmap]
rs13403102	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13404037	0.89[JPT][hapmap]
rs13420582	0.95[AFR][1000 genomes]
rs17363260	0.89[JPT][hapmap]
rs17454311	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2289993	0.89[JPT][hapmap];0.85[YRI][hapmap]
rs2289994	0.89[JPT][hapmap];0.85[YRI][hapmap]
rs35539795	0.83[AFR][1000 genomes]
rs58887763	0.81[AFR][1000 genomes]
rs6743412	0.94[CEU][hapmap]
rs6759983	0.94[CEU][hapmap]
rs7569887	0.88[CEU][hapmap]
rs7601366	0.84[CEU][hapmap];0.89[JPT][hapmap]
rs7608745	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs9288026	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv3061	chr2:180057194-180095718	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv1840933	chr2:180068214-180089983	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv3341806	chr2:180070495-180093344	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv583865	chr2:180072586-180088968	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv1798738	chr2:180084168-180100584	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9288025	SESTD1	cis	multi-tissue	Pritchard

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180067600-180097600	Weak transcription	Primary B cells from cord blood	blood
2	chr2:180067600-180104600	Weak transcription	Fetal Kidney	kidney
3	chr2:180068000-180103800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:180068400-180092800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:180072400-180090400	Weak transcription	Pancreas	Pancrea
6	chr2:180083800-180088800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:180083800-180088800	Weak transcription	Fetal Heart	heart
8	chr2:180083800-180089000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:180083800-180089000	Weak transcription	HepG2	liver
10	chr2:180083800-180089200	Weak transcription	Psoas Muscle	Psoas
11	chr2:180083800-180090400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:180083800-180091000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:180083800-180092000	Weak transcription	Aorta	Aorta
14	chr2:180083800-180102200	Weak transcription	HMEC	breast
15	chr2:180084000-180088800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:180084000-180089000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:180084000-180089400	Weak transcription	Right Ventricle	heart
18	chr2:180084000-180090400	Weak transcription	Right Atrium	heart
19	chr2:180084000-180091000	Weak transcription	Small Intestine	intestine
20	chr2:180084200-180089000	Weak transcription	Brain Angular Gyrus	brain
21	chr2:180084200-180089000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:180084200-180089000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:180084200-180091000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:180084400-180089000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:180085200-180091200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:180085400-180091200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:180085600-180088800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:180085600-180089000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr2:180086400-180089200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:180087000-180088800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:180087000-180088800	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:180087000-180089000	Weak transcription	Adipose Nuclei	Adipose
33	chr2:180087200-180088800	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:180087200-180097600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr2:180087400-180089000	Weak transcription	Brain Anterior Caudate	brain
36	chr2:180087400-180094800	Weak transcription	Osteobl	bone
37	chr2:180087600-180088600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:180087600-180091000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:180087600-180095800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:180088000-180089000	Weak transcription	Brain Substantia Nigra	brain
41	chr2:180088400-180089200	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr2:180088400-180093000	Enhancers	Brain Cingulate Gyrus	brain

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