Variant report

Variant	rs1907421
Chromosome Location	chr2:180132657-180132658
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr2:180132581-180132664	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:180127590..180133149-chr2:180134052..180141026,12	MCF-7	breast:
2	chr2:180127197..180131104-chr2:180131643..180133525,5	MCF-7	breast:
3	chr2:180132248..180134762-chr2:180137452..180139078,2	MCF-7	breast:

Variant related genes	Relation type
SESTD1	TF binding region
ENSG00000187231	Chromatin interaction
ENSG00000237477	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10170520	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10174774	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10186198	0.84[EUR][1000 genomes]
rs10205999	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10439299	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10930858	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1158872	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11884516	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11894870	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11898291	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12997314	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13026497	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13383965	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13391602	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13418701	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2289992	0.81[EUR][1000 genomes]
rs4585064	0.82[EUR][1000 genomes]
rs6433757	0.81[EUR][1000 genomes]
rs6433760	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6433761	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6433764	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6433769	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6707081	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6734121	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6736098	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6742739	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6756326	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7562730	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7579536	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7585600	0.82[EUR][1000 genomes]
rs7608882	0.81[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
rs1907421	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180130000-180132800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:180130000-180133000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:180130000-180135200	Weak transcription	Brain Angular Gyrus	brain
4	chr2:180130000-180137200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:180130000-180138000	Weak transcription	Gastric	stomach
6	chr2:180130000-180138200	Weak transcription	Aorta	Aorta
7	chr2:180130000-180141000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:180130000-180141200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:180130200-180132800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:180130200-180133000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr2:180130200-180133000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:180130200-180133000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:180130200-180133000	Weak transcription	A549	lung
14	chr2:180130200-180133000	Weak transcription	NHDF-Ad	bronchial
15	chr2:180130200-180133200	Weak transcription	Brain Hippocampus Middle	brain
16	chr2:180130200-180136200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:180130200-180137200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:180130200-180137200	Weak transcription	NH-A	brain
19	chr2:180130400-180132800	Weak transcription	HMEC	breast
20	chr2:180130400-180132800	Weak transcription	HUVEC	blood vessel
21	chr2:180130400-180133000	Weak transcription	Brain Substantia Nigra	brain
22	chr2:180130400-180133200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:180130400-180136000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:180130400-180137400	Weak transcription	Fetal Intestine Large	intestine
25	chr2:180130400-180138400	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:180130400-180139200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:180130600-180132800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:180130600-180133000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:180130600-180138200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:180130800-180132800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr2:180130800-180132800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:180130800-180132800	Weak transcription	Osteobl	bone
33	chr2:180130800-180133000	Weak transcription	Adipose Nuclei	Adipose
34	chr2:180130800-180133200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr2:180130800-180135400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr2:180131000-180132800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr2:180131000-180132800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:180131000-180133000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:180131000-180133200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:180131200-180133200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:180131200-180133200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr2:180131800-180132800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr2:180132200-180134200	Enhancers	Hela-S3	cervix
44	chr2:180132600-180133400	Enhancers	GM12878-XiMat	blood
45	chr2:180132600-180133600	Enhancers	Placenta	Placenta
46	chr2:180132600-180133600	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr2:180132600-180133800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:180132600-180134000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:180132600-180134000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:180132600-180134000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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