Variant report

Variant	rs2241806
Chromosome Location	chr3:53901611-53901612
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	chr3:53901391..53905529-chr3:53913413..53917026,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222888	Chromatin interaction
ENSG00000113812	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1020082	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1134091	0.91[EUR][1000 genomes]
rs12632292	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17053568	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17053590	1.00[CEU][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs1982171	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2276840	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs2276843	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2276844	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2276845	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2289203	1.00[CEU][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs2304575	0.96[EUR][1000 genomes]
rs2304576	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2884631	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3017	0.81[CEU][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs3733075	0.84[CEU][hapmap];0.82[CHD][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3733079	0.87[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3733083	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3821868	0.87[EUR][1000 genomes]
rs3821869	0.84[CEU][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs41292476	0.89[EUR][1000 genomes]
rs4141606	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs45511795	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687594	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687753	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs4687756	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4687758	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4687760	0.86[EUR][1000 genomes]
rs55917919	0.92[EUR][1000 genomes]
rs56743403	0.93[EUR][1000 genomes]
rs57398949	0.96[EUR][1000 genomes]
rs62253003	0.80[EUR][1000 genomes]
rs62253004	0.80[EUR][1000 genomes]
rs6445612	0.81[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs709324	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73078007	0.83[EUR][1000 genomes]
rs9840445	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs9849951	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9850063	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860367	0.88[EUR][1000 genomes]
rs9880056	0.81[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs999515	0.96[CEU][hapmap];0.90[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2241806	ACTR8	cis	cerebellum	SCAN
rs2241806	ACTR8	cis	lymphoblastoid	seeQTL
rs2241806	ACTR8	cis	Thyroid	GTEx
rs2241806	DCP1A	cis	lymphoblastoid	seeQTL
rs2241806	SFMBT1	cis	cerebellum	SCAN
rs2241806	PHF7	cis	cerebellum	SCAN
rs2241806	ACTR8	cis	parietal	SCAN
rs2241806	IL17RB	cis	cerebellum	SCAN
rs2241806	IL17RB	cis	parietal	SCAN
rs2241806	SELK	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53888400-53914600	Weak transcription	Stomach Mucosa	stomach
2	chr3:53889600-53913800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:53890000-53904000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:53890400-53903600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:53890800-53914600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:53891000-53914200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:53891000-53914200	Strong transcription	Duodenum Mucosa	Duodenum
8	chr3:53891200-53910800	Strong transcription	Fetal Stomach	stomach
9	chr3:53891400-53914200	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:53891600-53904000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr3:53891800-53912800	Strong transcription	Brain Germinal Matrix	brain
12	chr3:53892000-53914400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:53892200-53912400	Strong transcription	Fetal Brain Female	brain
14	chr3:53892200-53914000	Strong transcription	Adipose Nuclei	Adipose
15	chr3:53892200-53914400	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:53892200-53914600	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:53892400-53904800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:53892400-53906200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:53892400-53913000	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:53892400-53913800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:53892400-53914200	Strong transcription	Stomach Smooth Muscle	stomach
22	chr3:53892400-53914400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:53892600-53914200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:53892600-53914400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:53892600-53914400	Strong transcription	Fetal Muscle Leg	muscle
26	chr3:53892800-53914200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:53892800-53914200	Strong transcription	Fetal Muscle Trunk	muscle
28	chr3:53892800-53914200	Strong transcription	Thymus	Thymus
29	chr3:53892800-53914400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:53892800-53914600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr3:53893000-53914000	Strong transcription	Placenta	Placenta
32	chr3:53893000-53914400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:53893200-53914000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:53893200-53914200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:53893200-53914200	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:53893200-53914200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:53893200-53914600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:53893400-53902600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:53893400-53908200	Weak transcription	K562	blood
40	chr3:53893400-53914200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:53893800-53912800	Strong transcription	Brain Anterior Caudate	brain
42	chr3:53894200-53914400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:53894400-53914000	Strong transcription	Primary T cells from cord blood	blood
44	chr3:53894400-53914400	Strong transcription	Fetal Thymus	thymus
45	chr3:53894800-53914200	Strong transcription	Primary hematopoietic stem cells	blood
46	chr3:53894800-53914200	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr3:53895000-53902400	Strong transcription	Fetal Lung	lung
48	chr3:53895000-53914000	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr3:53895000-53914200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr3:53895000-53914400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links