Variant report

Variant	rs3766928
Chromosome Location	chr1:225601647-225601648
allele	C/T
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	CTCF	chr1:225601460-225601690	HRE	kidney:	n/a	n/a
2	POLR2A	chr1:225592461-225603516	K562	blood:	n/a	n/a
3	CTCF	chr1:225601580-225601730	RPTEC	kidney:	n/a	n/a
4	POLR2A	chr1:225601477-225602016	K562	blood:	n/a	n/a
5	POLR2A	chr1:225601438-225602025	K562	blood:	n/a	n/a
6	FOXA2	chr1:225601546-225601777	HepG2	liver:	n/a	n/a
7	CTCF	chr1:225601620-225601770	GM12869	blood:	n/a	n/a
8	FOXA1	chr1:225601478-225601836	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:225601406-225602786	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225600905..225602829-chr1:225614206..225615889,2	MCF-7	breast:

Variant related genes	Relation type
LBR	TF binding region
ENSG00000143815	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10495240	0.87[CEU][hapmap];0.85[AMR][1000 genomes]
rs10495241	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1056608	0.83[YRI][hapmap]
rs10753404	0.82[CEU][hapmap]
rs10753405	0.82[ASW][hapmap];0.82[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs10799307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915820	0.84[AMR][1000 genomes]
rs10915823	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580119	0.80[CEU][hapmap]
rs11799479	0.88[CHB][hapmap]
rs12028429	0.80[CEU][hapmap]
rs1538930	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1538933	0.88[ASW][hapmap];0.82[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs3766929	0.88[CHB][hapmap];0.80[YRI][hapmap]
rs3856155	0.88[ASW][hapmap];0.82[CEU][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap]
rs3949347	0.82[ASW][hapmap];0.82[CEU][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs5015446	0.81[CEU][hapmap]
rs6426069	0.85[AMR][1000 genomes]
rs6426071	0.85[AMR][1000 genomes]
rs6426073	0.85[AMR][1000 genomes]
rs7539172	0.82[ASW][hapmap];0.87[CEU][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes]
rs950210	0.81[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3766928	SLC30A10	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225582200-225610400	Strong transcription	Fetal Thymus	thymus
2	chr1:225583400-225601800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:225583600-225602200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:225584000-225603800	Weak transcription	Psoas Muscle	Psoas
5	chr1:225584200-225610600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:225584800-225609800	Strong transcription	Dnd41	blood
7	chr1:225584800-225610400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:225585000-225609800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:225585000-225609800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:225585000-225609800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:225585000-225610400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:225585200-225609800	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:225585800-225610000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:225585800-225610000	Strong transcription	K562	blood
15	chr1:225585800-225610400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr1:225586000-225607000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:225587600-225607000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:225587600-225607800	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:225587800-225610000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:225588200-225605400	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr1:225588200-225608200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:225588200-225610200	Strong transcription	Osteobl	bone
23	chr1:225588400-225604200	Strong transcription	HUVEC	blood vessel
24	chr1:225588600-225608400	Strong transcription	Hela-S3	cervix
25	chr1:225588600-225609800	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr1:225589000-225607400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:225590200-225610000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:225590600-225607200	Strong transcription	Primary T cells from cord blood	blood
29	chr1:225590600-225607400	Strong transcription	Thymus	Thymus
30	chr1:225590600-225607800	Strong transcription	Fetal Muscle Leg	muscle
31	chr1:225590600-225608400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:225590800-225608200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr1:225591000-225604000	Strong transcription	Fetal Stomach	stomach
34	chr1:225591800-225608200	Strong transcription	Brain Germinal Matrix	brain
35	chr1:225592800-225607400	Strong transcription	Primary hematopoietic stem cells	blood
36	chr1:225593000-225602600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:225593000-225610800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:225593400-225602200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr1:225594600-225607200	Strong transcription	NHEK	skin
40	chr1:225595400-225610400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:225595600-225607600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:225595800-225608400	Strong transcription	Fetal Brain Female	brain
43	chr1:225596200-225607600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:225596800-225607000	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr1:225596800-225607600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:225596800-225610600	Strong transcription	HSMM	muscle
47	chr1:225597000-225607200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr1:225597200-225601800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr1:225597400-225602200	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:225597400-225603400	Strong transcription	NHDF-Ad	bronchial

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