Variant report

Variant	rs9864057
Chromosome Location	chr3:53275777-53275778
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53266350..53272175-chr3:53273806..53279972,8	K562	blood:
2	chr3:53189219..53190940-chr3:53274136..53276946,2	MCF-7	breast:
3	chr3:53268931..53277907-chr3:53285563..53291617,11	MCF-7	breast:
4	chr3:53268759..53271558-chr3:53275387..53277889,3	MCF-7	breast:
5	chr3:53267066..53270422-chr3:53274180..53278623,4	K562	blood:

Variant related genes	Relation type
ENSG00000163932	Chromatin interaction
ENSG00000163931	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10433617	0.83[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10433618	0.83[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1108506	0.83[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs11551405	0.83[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes]
rs17030933	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17030934	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17234092	0.90[GIH][hapmap]
rs17234771	0.83[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41275543	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56654807	0.84[AMR][1000 genomes]
rs58558806	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59145995	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62255989	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62255993	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62255994	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62255999	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62256000	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62256003	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62256009	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62256043	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62256049	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62256050	0.81[EUR][1000 genomes]
rs62256962	0.82[AMR][1000 genomes]
rs73080266	0.82[AMR][1000 genomes]
rs73080271	0.82[AMR][1000 genomes]
rs73080273	0.82[AMR][1000 genomes]
rs7622159	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9826552	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs9830594	0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9830895	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9846315	0.83[EUR][1000 genomes]
rs9850440	0.83[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[EUR][1000 genomes];0.90[ASN][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	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9864057	SFMBT1	cis	parietal	SCAN
rs9864057	PRKCD	cis	parietal	SCAN
rs9864057	TLR9	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53256400-53276400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:53256400-53276600	Strong transcription	Fetal Brain Female	brain
3	chr3:53256400-53276800	Strong transcription	Fetal Stomach	stomach
4	chr3:53256800-53276600	Strong transcription	Thymus	Thymus
5	chr3:53256800-53277000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:53256800-53277000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:53257000-53276800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:53257000-53276800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:53257000-53277800	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:53257200-53276200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:53257200-53276600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:53257400-53276200	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr3:53257400-53276600	Strong transcription	Primary B cells from peripheral blood	blood
14	chr3:53257400-53277200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:53257400-53278800	Strong transcription	Primary T cells from cord blood	blood
16	chr3:53257400-53280200	Strong transcription	Dnd41	blood
17	chr3:53257600-53276400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:53257600-53276800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:53257800-53276600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr3:53258200-53276800	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr3:53258400-53276800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr3:53258600-53276600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:53266800-53276600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:53266800-53279000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:53268200-53276600	Strong transcription	Primary B cells from cord blood	blood
26	chr3:53269400-53276600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:53269600-53280400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:53270000-53280000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:53270600-53276600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:53270800-53278000	Strong transcription	Fetal Thymus	thymus
31	chr3:53271000-53275800	Strong transcription	Brain Hippocampus Middle	brain
32	chr3:53271000-53275800	Weak transcription	Psoas Muscle	Psoas
33	chr3:53271000-53276000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:53271000-53276600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:53271200-53275800	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:53271200-53277000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:53271200-53277200	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:53271800-53276400	Strong transcription	Primary hematopoietic stem cells	blood
39	chr3:53271800-53276800	Genic enhancers	Fetal Muscle Leg	muscle
40	chr3:53272000-53276000	Genic enhancers	Fetal Muscle Trunk	muscle
41	chr3:53272000-53276200	Genic enhancers	Placenta	Placenta
42	chr3:53272000-53278800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:53272000-53278800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:53272200-53276200	Strong transcription	Rectal Smooth Muscle	rectum
45	chr3:53272200-53276400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:53272200-53276400	Genic enhancers	Monocytes-CD14+_RO01746	blood
47	chr3:53272200-53278800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:53272400-53275800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:53272400-53282200	Genic enhancers	Primary monocytes fromperipheralblood	blood
50	chr3:53272600-53276200	Strong transcription	Aorta	Aorta

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