Variant report

Variant	rs7562730
Chromosome Location	chr2:180125157-180125158
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:180116382..180118315-chr2:180123410..180126262,2	MCF-7	breast:
2	chr2:180115892..180117617-chr2:180123291..180126152,2	K562	blood:
3	chr2:180114550..180116150-chr2:180123274..180125911,2	MCF-7	breast:
4	chr2:180118975..180121494-chr2:180124484..180126493,2	K562	blood:
5	chr2:180115733..180117570-chr2:180124952..180126888,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10170520	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10174774	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10186198	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10204985	0.84[AFR][1000 genomes]
rs10205999	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10439299	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10930858	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158872	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884516	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11894870	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898291	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12105846	0.84[AFR][1000 genomes]
rs12997314	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13026497	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13383965	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13391602	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13418701	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1907421	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289992	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4585064	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs58887763	0.80[EUR][1000 genomes]
rs6433757	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6433760	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6433761	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6433764	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6433769	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6707081	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6734121	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736098	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6742739	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6756326	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579536	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7585600	0.83[EUR][1000 genomes]
rs7608882	0.82[AFR][1000 genomes];0.82[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	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
2	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
rs7562730	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180091800-180127200	Weak transcription	Fetal Lung	lung
2	chr2:180102800-180127800	Weak transcription	Psoas Muscle	Psoas
3	chr2:180112400-180126200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:180112600-180126800	Weak transcription	Hela-S3	cervix
5	chr2:180115400-180127600	Weak transcription	NHLF	lung
6	chr2:180117400-180126200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:180117800-180126400	Weak transcription	Small Intestine	intestine
8	chr2:180118000-180125200	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:180118600-180126200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr2:180118800-180127600	Weak transcription	HSMM	muscle
11	chr2:180118800-180128200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:180119400-180128200	Weak transcription	Pancreas	Pancrea
13	chr2:180119600-180126200	Weak transcription	Brain Anterior Caudate	brain
14	chr2:180120000-180127400	Weak transcription	Brain Angular Gyrus	brain
15	chr2:180120200-180127200	Weak transcription	Fetal Kidney	kidney
16	chr2:180120200-180127600	Weak transcription	Fetal Stomach	stomach
17	chr2:180120400-180126800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:180122600-180127400	Enhancers	Adipose Nuclei	Adipose
19	chr2:180123600-180126400	Weak transcription	Fetal Brain Male	brain
20	chr2:180123600-180126800	Weak transcription	Brain Substantia Nigra	brain
21	chr2:180123800-180125800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr2:180123800-180127600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:180123800-180127800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:180123800-180127800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:180123800-180128000	Enhancers	Primary B cells from peripheral blood	blood
26	chr2:180124000-180125200	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:180124000-180127400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:180124200-180126400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:180124200-180126400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:180124200-180126400	Enhancers	NHEK	skin
31	chr2:180124400-180125200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:180124400-180126000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:180124400-180126600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:180124400-180127000	Enhancers	HMEC	breast
35	chr2:180124400-180127600	Weak transcription	Fetal Intestine Small	intestine
36	chr2:180124600-180125200	Enhancers	HepG2	liver
37	chr2:180124600-180127200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:180124800-180127400	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr2:180125000-180125200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:180125000-180125200	Enhancers	Primary T cells fromperipheralblood	blood
41	chr2:180125000-180125200	Enhancers	Aorta	Aorta
42	chr2:180125000-180125200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
43	chr2:180125000-180125400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:180125000-180125400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:180125000-180125400	Enhancers	Left Ventricle	heart
46	chr2:180125000-180125400	Enhancers	Right Atrium	heart
47	chr2:180125000-180125600	Enhancers	Primary B cells from cord blood	blood
48	chr2:180125000-180126000	Enhancers	GM12878-XiMat	blood
49	chr2:180125000-180126400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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