Variant report

Variant	rs1476347
Chromosome Location	chr1:166815587-166815588
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:166814063..166816782-chr1:166816972..166818732,3	MCF-7	breast:
2	chr1:166812541..166816415-chr1:166843995..166846618,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152382	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10800270	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10800276	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap]
rs11576455	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11583927	0.82[CHB][hapmap]
rs11584352	0.87[EUR][1000 genomes]
rs12062326	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12562794	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2075946	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2235184	0.83[CEU][hapmap]
rs2280995	0.94[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2294195	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3820387	1.00[CEU][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4657609	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4657613	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap]
rs56229522	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6427047	0.83[CEU][hapmap]
rs9633326	0.82[CHB][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	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1476347	RGS4	cis	parietal	SCAN
rs1476347	DUSP12	cis	cerebellum	SCAN
rs1476347	B4GALT3	cis	parietal	SCAN
rs1476347	FAM78B	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166809600-166844400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:166810000-166815800	Genic enhancers	Spleen	Spleen
3	chr1:166810200-166820600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:166810400-166815800	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:166810400-166817200	Genic enhancers	Left Ventricle	heart
6	chr1:166810400-166820600	Strong transcription	Ovary	ovary
7	chr1:166810400-166822000	Strong transcription	Thymus	Thymus
8	chr1:166810400-166828600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:166810600-166815800	Enhancers	Right Atrium	heart
10	chr1:166810600-166820200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:166810600-166823600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:166810600-166824400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:166810600-166825600	Strong transcription	NHLF	lung
14	chr1:166810600-166828200	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:166810600-166829000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:166810600-166829400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:166810600-166834800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:166810600-166838800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:166810800-166817200	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:166810800-166819200	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr1:166810800-166824000	Strong transcription	NHEK	skin
22	chr1:166810800-166825000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:166810800-166827400	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr1:166810800-166827800	Strong transcription	A549	lung
25	chr1:166810800-166828600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:166810800-166828800	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:166810800-166828800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:166810800-166832400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:166810800-166834200	Strong transcription	Fetal Stomach	stomach
30	chr1:166810800-166835200	Strong transcription	K562	blood
31	chr1:166810800-166839200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:166810800-166839200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:166811000-166817800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr1:166811000-166835600	Strong transcription	Primary B cells from cord blood	blood
35	chr1:166811200-166834600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:166811200-166839800	Strong transcription	Primary T cells from cord blood	blood
37	chr1:166811400-166827400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:166811400-166829800	Strong transcription	Primary hematopoietic stem cells	blood
39	chr1:166811600-166818800	Weak transcription	Small Intestine	intestine
40	chr1:166811600-166823600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:166811600-166827400	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:166811800-166838600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:166811800-166838600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:166812000-166815800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:166812000-166825000	Strong transcription	HepG2	liver
46	chr1:166812000-166838400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr1:166812000-166838800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr1:166812200-166838800	Strong transcription	Fetal Thymus	thymus
49	chr1:166812400-166820800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:166812600-166821800	Strong transcription	GM12878-XiMat	blood

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