Variant report

Variant	rs13414296
Chromosome Location	chr2:180091561-180091562
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	chr2:180091158..180092678-chr2:180127658..180130558,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187231	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10164707	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10164814	0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10176829	0.83[AMR][1000 genomes]
rs10177122	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10177402	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10181291	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10181464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10182477	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10185803	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10188759	0.84[EUR][1000 genomes]
rs10194420	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10194534	0.93[EUR][1000 genomes]
rs10196366	0.86[ASN][1000 genomes]
rs10204985	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10209183	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10209887	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10439300	0.99[AFR][1000 genomes]
rs10930859	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12105846	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12617002	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12621023	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12621115	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12622075	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12623243	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12693179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12693181	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12693183	0.81[ASN][1000 genomes]
rs12987285	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13020645	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13382185	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13384403	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13392996	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13396340	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13417919	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2007593	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28838656	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57098667	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433770	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67043078	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6731614	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6743412	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759983	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7569887	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601366	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7608745	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9288026	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
6	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
rs13414296	SESTD1	cis	multi-tissue	Pritchard
rs13414296	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

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	chr2:180083800-180092000	Weak transcription	Aorta	Aorta
6	chr2:180083800-180102200	Weak transcription	HMEC	breast
7	chr2:180087200-180097600	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr2:180087400-180094800	Weak transcription	Osteobl	bone
9	chr2:180087600-180095800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:180088400-180093000	Enhancers	Brain Cingulate Gyrus	brain
11	chr2:180088600-180092200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:180088800-180098400	Weak transcription	Spleen	Spleen
13	chr2:180089000-180091800	Enhancers	Brain Angular Gyrus	brain
14	chr2:180089000-180093000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:180089000-180093000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr2:180089000-180093000	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr2:180089000-180093400	Enhancers	Brain Anterior Caudate	brain
18	chr2:180089200-180092400	Weak transcription	Ovary	ovary
19	chr2:180089600-180092000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr2:180089600-180095000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:180089600-180115200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:180089800-180091600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:180089800-180091600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:180089800-180095000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:180089800-180095000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr2:180089800-180100200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:180089800-180100200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:180089800-180102000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:180090000-180091600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:180090000-180092600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr2:180090000-180093800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:180090000-180098400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:180090000-180102000	Weak transcription	Fetal Muscle Leg	muscle
34	chr2:180090200-180092200	Enhancers	Brain Germinal Matrix	brain
35	chr2:180090400-180091600	Enhancers	Right Atrium	heart
36	chr2:180090400-180091800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr2:180090400-180092600	Enhancers	Liver	Liver
38	chr2:180090400-180092800	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr2:180090400-180093000	Enhancers	Adipose Nuclei	Adipose
40	chr2:180090600-180102000	Weak transcription	Psoas Muscle	Psoas
41	chr2:180090600-180102400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:180091000-180091600	Enhancers	Muscle Satellite Cultured Cells	--
43	chr2:180091000-180091600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr2:180091000-180091600	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr2:180091000-180091800	Enhancers	Fetal Brain Male	brain
46	chr2:180091000-180091800	Enhancers	Small Intestine	intestine
47	chr2:180091000-180092000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:180091000-180092800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:180091000-180093400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:180091200-180091600	Weak transcription	Colon Smooth Muscle	Colon

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