Variant report

Variant	rs12693179
Chromosome Location	chr2:180087367-180087368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10164707	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10164814	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10176829	0.83[AMR][1000 genomes]
rs10177122	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10177402	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10181291	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10181464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182477	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10185803	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10188759	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs10194420	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10194534	0.90[EUR][1000 genomes]
rs10196366	0.88[ASN][1000 genomes]
rs10204985	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10209183	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10209887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10439300	0.90[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs10803924	0.89[JPT][hapmap]
rs10930859	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12105846	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12617002	0.82[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12621023	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12621115	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12622075	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12623243	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12693181	0.82[EUR][1000 genomes]
rs12693183	0.81[ASN][1000 genomes]
rs12987285	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13020645	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13382185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13384403	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13392996	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13396340	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13414296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13417919	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17454311	0.95[CEU][hapmap];0.90[JPT][hapmap]
rs2007593	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2166534	0.83[YRI][hapmap]
rs28838656	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs340320	0.86[JPT][hapmap]
rs340332	0.90[JPT][hapmap]
rs340334	0.90[JPT][hapmap]
rs4894082	0.82[YRI][hapmap]
rs57098667	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6433770	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67043078	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6731614	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6743412	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6759983	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7569887	0.84[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7601366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608745	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9288025	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs9288026	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12693179	SESTD1	cis	multi-tissue	Pritchard
rs12693179	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 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	chr2:180085600-180088400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr2:180085600-180088800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:180085600-180089000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr2:180086400-180089200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:180086600-180087600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:180086600-180088000	Enhancers	Brain Substantia Nigra	brain
33	chr2:180086800-180087400	Enhancers	Brain Anterior Caudate	brain
34	chr2:180086800-180087400	Enhancers	Osteobl	bone
35	chr2:180086800-180087600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:180087000-180088800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:180087000-180088800	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:180087000-180089000	Weak transcription	Adipose Nuclei	Adipose
39	chr2:180087200-180087600	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr2:180087200-180088800	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:180087200-180097600	Weak transcription	Monocytes-CD14+_RO01746	blood

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