Variant report

Variant	rs13026497
Chromosome Location	chr2:180104255-180104256
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	chr2:180099965..180101717-chr2:180103234..180105570,2	K562	blood:
2	chr2:180099014..180101971-chr2:180103448..180105283,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10170520	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10174774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10186198	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10192426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes]
rs10204985	0.84[AFR][1000 genomes]
rs10205390	0.83[JPT][hapmap];0.83[YRI][hapmap]
rs10205999	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10439299	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10930858	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1158872	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11884516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11894870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11898291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12105846	0.84[AFR][1000 genomes]
rs12997314	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13383965	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13391602	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13418701	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1374378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1446674	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap]
rs1907421	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1979053	0.82[EUR][1000 genomes]
rs2008989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs2008999	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs2289992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2847	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes]
rs4585064	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6433757	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6433760	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433761	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6433764	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6433769	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6707081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6734121	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6736098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6742739	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6743405	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes]
rs6756326	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6757681	0.85[YRI][hapmap]
rs7562730	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7579536	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7585600	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes]
rs7608882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs873023	0.81[YRI][hapmap]
rs9288022	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv834472	chr2:180091670-180220448	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13026497	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180067600-180104600	Weak transcription	Fetal Kidney	kidney
2	chr2:180089600-180115200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:180091200-180104600	Weak transcription	Right Ventricle	heart
4	chr2:180091800-180127200	Weak transcription	Fetal Lung	lung
5	chr2:180092800-180104600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:180092800-180112400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:180093000-180107800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:180098000-180105200	Weak transcription	Fetal Thymus	thymus
9	chr2:180098600-180118600	Weak transcription	Pancreas	Pancrea
10	chr2:180100800-180104400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:180100800-180104800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:180100800-180105000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:180100800-180105200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:180101200-180105200	Weak transcription	Aorta	Aorta
15	chr2:180101200-180112200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr2:180101800-180105000	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr2:180101800-180105600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:180101800-180107000	Enhancers	Brain Substantia Nigra	brain
19	chr2:180102000-180105000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:180102000-180105200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:180102000-180105400	Enhancers	Adipose Nuclei	Adipose
22	chr2:180102000-180105800	Enhancers	Brain Cingulate Gyrus	brain
23	chr2:180102200-180104400	Enhancers	NHDF-Ad	bronchial
24	chr2:180102200-180104600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr2:180102200-180105000	Enhancers	HMEC	breast
26	chr2:180102200-180105800	Enhancers	HUVEC	blood vessel
27	chr2:180102400-180105600	Enhancers	Colon Smooth Muscle	Colon
28	chr2:180102400-180106200	Enhancers	Brain Hippocampus Middle	brain
29	chr2:180102600-180104600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:180102600-180105000	Enhancers	Primary T cells from cord blood	blood
31	chr2:180102600-180105200	Weak transcription	Fetal Muscle Leg	muscle
32	chr2:180102800-180104600	Weak transcription	Brain Angular Gyrus	brain
33	chr2:180102800-180104800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:180102800-180104800	Enhancers	Fetal Intestine Large	intestine
35	chr2:180102800-180104800	Enhancers	Fetal Intestine Small	intestine
36	chr2:180102800-180105200	Weak transcription	HSMMtube	muscle
37	chr2:180102800-180105400	Weak transcription	Left Ventricle	heart
38	chr2:180102800-180127800	Weak transcription	Psoas Muscle	Psoas
39	chr2:180103000-180104600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr2:180103000-180105800	Enhancers	Hela-S3	cervix
41	chr2:180103000-180112200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:180103200-180104600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:180103200-180104800	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr2:180103200-180105200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:180103200-180105200	Enhancers	A549	lung
46	chr2:180103200-180105200	Enhancers	NHEK	skin
47	chr2:180103200-180106200	Enhancers	Dnd41	blood
48	chr2:180103200-180116000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr2:180103400-180105000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:180103400-180105400	Enhancers	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links