Variant report

Variant	rs13389956
Chromosome Location	chr2:180112641-180112642
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:180111560..180114126-chr2:180128041..180130307,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187231	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10170430	0.94[ASN][1000 genomes]
rs10194534	0.99[AFR][1000 genomes]
rs10196577	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10197425	0.97[ASN][1000 genomes]
rs10208593	0.91[ASN][1000 genomes]
rs10439300	0.91[EUR][1000 genomes]
rs10930857	0.91[ASN][1000 genomes]
rs12621023	0.84[AFR][1000 genomes]
rs12693180	1.00[ASN][1000 genomes]
rs12989055	1.00[ASN][1000 genomes]
rs13420582	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13427714	0.88[ASN][1000 genomes]
rs28763731	0.84[EUR][1000 genomes]
rs35539795	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs58887763	0.92[AFR][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
rs13389956	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180089600-180115200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:180091800-180127200	Weak transcription	Fetal Lung	lung
3	chr2:180098600-180118600	Weak transcription	Pancreas	Pancrea
4	chr2:180102800-180127800	Weak transcription	Psoas Muscle	Psoas
5	chr2:180103200-180116000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:180105600-180116000	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:180105600-180120000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:180106200-180116400	Weak transcription	Small Intestine	intestine
9	chr2:180107000-180115600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr2:180110000-180116800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:180110200-180124200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:180110600-180113400	Enhancers	HepG2	liver
13	chr2:180111200-180113000	Enhancers	Adipose Nuclei	Adipose
14	chr2:180111200-180120400	Enhancers	Primary B cells from peripheral blood	blood
15	chr2:180112000-180112800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr2:180112000-180112800	Enhancers	Brain Substantia Nigra	brain
17	chr2:180112200-180112800	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr2:180112200-180112800	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr2:180112200-180120000	Weak transcription	Fetal Kidney	kidney
20	chr2:180112400-180112800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr2:180112400-180112800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:180112400-180112800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:180112400-180112800	Enhancers	Brain Angular Gyrus	brain
24	chr2:180112400-180113000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:180112400-180113400	Enhancers	Dnd41	blood
26	chr2:180112400-180126200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr2:180112600-180112800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr2:180112600-180113000	Active TSS	GM12878-XiMat	blood
29	chr2:180112600-180115200	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr2:180112600-180116400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:180112600-180117600	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:180112600-180118400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:180112600-180125000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr2:180112600-180126800	Weak transcription	Hela-S3	cervix

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