Variant report

Variant	rs10208593
Chromosome Location	chr2:180088968-180088969
allele	A/C
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: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10084229	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10084475	0.85[AFR][1000 genomes]
rs10170430	0.97[ASN][1000 genomes]
rs10173710	0.87[AFR][1000 genomes]
rs10196577	0.97[ASN][1000 genomes]
rs10197425	0.89[CHD][hapmap];0.94[ASN][1000 genomes]
rs10205477	0.85[ASN][1000 genomes]
rs10439300	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs10803924	0.88[JPT][hapmap]
rs10930855	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10930856	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs10930857	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12621023	0.89[JPT][hapmap];0.89[YRI][hapmap]
rs12693175	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12693178	0.92[YRI][hapmap]
rs12693180	0.91[ASN][1000 genomes]
rs12989055	0.91[ASN][1000 genomes]
rs12997079	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs13022867	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs13029576	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13389956	0.91[ASN][1000 genomes]
rs13396334	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13403231	0.88[ASN][1000 genomes]
rs13404037	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13420582	0.97[ASN][1000 genomes]
rs13427714	0.84[ASN][1000 genomes]
rs17363260	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs17363267	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs17454311	0.86[ASW][hapmap];0.89[JPT][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs1900338	0.85[AFR][1000 genomes]
rs1968618	0.89[YRI][hapmap]
rs2289993	0.86[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs2289994	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[YRI][hapmap]
rs28763731	0.96[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs340320	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs340332	0.89[JPT][hapmap]
rs340334	0.89[JPT][hapmap]
rs34728717	0.83[AFR][1000 genomes]
rs35539795	0.83[ASN][1000 genomes]
rs4894081	0.92[YRI][hapmap]
rs56109193	0.85[AFR][1000 genomes]
rs56181927	0.88[ASN][1000 genomes]
rs67028844	0.88[ASN][1000 genomes]
rs9288025	0.89[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10208593	SESTD1	cis	cerebellum	SCAN
rs10208593	SESTD1	Cis_1M	lymphoblastoid	RTeQTL
rs10208593	SESTD1	cis	parietal	SCAN
rs10208593	SESTD1	cis	multi-tissue	Pritchard

Chromatin state (count:47 , 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	chr2:180083800-180089000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:180083800-180089000	Weak transcription	HepG2	liver
8	chr2:180083800-180089200	Weak transcription	Psoas Muscle	Psoas
9	chr2:180083800-180090400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:180083800-180091000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:180083800-180092000	Weak transcription	Aorta	Aorta
12	chr2:180083800-180102200	Weak transcription	HMEC	breast
13	chr2:180084000-180089000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:180084000-180089400	Weak transcription	Right Ventricle	heart
15	chr2:180084000-180090400	Weak transcription	Right Atrium	heart
16	chr2:180084000-180091000	Weak transcription	Small Intestine	intestine
17	chr2:180084200-180089000	Weak transcription	Brain Angular Gyrus	brain
18	chr2:180084200-180089000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:180084200-180089000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:180084200-180091000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:180084400-180089000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr2:180085200-180091200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:180085400-180091200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:180085600-180089000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr2:180086400-180089200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:180087000-180089000	Weak transcription	Adipose Nuclei	Adipose
27	chr2:180087200-180097600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr2:180087400-180089000	Weak transcription	Brain Anterior Caudate	brain
29	chr2:180087400-180094800	Weak transcription	Osteobl	bone
30	chr2:180087600-180091000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:180087600-180095800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:180088000-180089000	Weak transcription	Brain Substantia Nigra	brain
33	chr2:180088400-180089200	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr2:180088400-180093000	Enhancers	Brain Cingulate Gyrus	brain
35	chr2:180088600-180089200	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr2:180088600-180092200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:180088800-180089200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:180088800-180089600	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr2:180088800-180089600	Enhancers	Fetal Heart	heart
40	chr2:180088800-180089600	Enhancers	Stomach Smooth Muscle	stomach
41	chr2:180088800-180089800	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr2:180088800-180089800	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr2:180088800-180090000	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr2:180088800-180090600	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr2:180088800-180090800	Enhancers	Brain Hippocampus Middle	brain
46	chr2:180088800-180091200	Enhancers	Colon Smooth Muscle	Colon
47	chr2:180088800-180098400	Weak transcription	Spleen	Spleen

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