Variant report

Variant	rs2047551
Chromosome Location	chr3:196007493-196007494
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:196005160..196007960-chr3:196014818..196016357,2	K562	blood:
2	chr3:196006494..196009381-chr3:196019431..196021993,2	K562	blood:

Variant related genes	Relation type
ENSG00000161217	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11929532	0.89[CHD][hapmap];0.85[JPT][hapmap]
rs12629949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12630070	0.85[JPT][hapmap]
rs12632779	0.81[JPT][hapmap];0.83[MEX][hapmap]
rs12634304	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12634587	0.81[JPT][hapmap]
rs12637288	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[ASN][1000 genomes]
rs1357289	0.85[CHD][hapmap]
rs1948690	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2047550	0.80[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap]
rs2088666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2270769	0.85[JPT][hapmap]
rs2293160	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs3772109	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4396926	0.97[ASN][1000 genomes]
rs4916421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4916424	0.89[CHD][hapmap];0.85[JPT][hapmap]
rs4916425	0.89[CHD][hapmap];0.85[JPT][hapmap]
rs4916456	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4916477	0.85[JPT][hapmap]
rs4916485	0.81[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap]
rs55996879	0.82[ASN][1000 genomes]
rs58297632	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs58945504	0.80[AMR][1000 genomes]
rs59289255	0.93[ASN][1000 genomes]
rs59352354	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61442465	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66487782	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66780758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66805306	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66927787	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67349960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6762272	0.89[CHD][hapmap];0.85[JPT][hapmap]
rs6766480	0.89[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs67784045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6778879	0.89[CHD][hapmap];0.85[JPT][hapmap]
rs68056570	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6809764	0.81[ASN][1000 genomes]
rs72611188	0.96[ASN][1000 genomes]
rs7625886	0.85[JPT][hapmap]
rs7636149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7639752	0.85[JPT][hapmap]
rs7640304	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs870339	0.94[CHB][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs939883	0.85[JPT][hapmap]
rs9714038	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
6	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
7	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
8	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
9	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
10	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
11	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
12	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
13	nsv878179	chr3:195929268-196019680	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
14	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
15	nsv878180	chr3:195946535-196066569	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
16	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
17	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
18	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
19	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2047551	OSTalpha	cis	cerebellum	SCAN
rs2047551	TCTEX1D2	cis	parietal	SCAN
rs2047551	MGC33212	cis	multi-tissue	Pritchard
rs2047551	PCYT1A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195965800-196012400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:195969600-196012400	Weak transcription	Fetal Brain Male	brain
3	chr3:195991800-196012400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:195996600-196012600	Weak transcription	Fetal Kidney	kidney
5	chr3:195997600-196007800	Weak transcription	Small Intestine	intestine
6	chr3:195997600-196010600	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:196000600-196011200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:196000600-196012400	Weak transcription	Fetal Brain Female	brain
9	chr3:196000600-196012600	Weak transcription	Fetal Lung	lung
10	chr3:196000600-196012800	Weak transcription	Ovary	ovary
11	chr3:196000600-196013800	Weak transcription	Aorta	Aorta
12	chr3:196001000-196011600	Weak transcription	Thymus	Thymus
13	chr3:196001000-196013800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:196001200-196011400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:196001200-196013600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:196001400-196013000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:196001400-196013200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:196001600-196013000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:196001800-196008000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:196001800-196010600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:196001800-196011600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:196001800-196012600	Weak transcription	Primary T cells from cord blood	blood
23	chr3:196001800-196012600	Weak transcription	Fetal Stomach	stomach
24	chr3:196002000-196011600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:196002200-196011800	Weak transcription	Dnd41	blood
26	chr3:196002200-196012600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:196002400-196011600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr3:196002400-196012600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr3:196004800-196008400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:196004800-196009800	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr3:196005000-196007600	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr3:196005000-196008000	Enhancers	Adipose Nuclei	Adipose
33	chr3:196005000-196008600	Enhancers	Stomach Mucosa	stomach
34	chr3:196005000-196009600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:196005000-196011200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:196005000-196013000	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr3:196005200-196008200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:196005200-196008200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:196005200-196008600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:196005200-196009200	Enhancers	Fetal Intestine Large	intestine
41	chr3:196005200-196009800	Enhancers	Liver	Liver
42	chr3:196005400-196007600	Enhancers	Right Atrium	heart
43	chr3:196005400-196008400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:196005600-196012400	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr3:196005800-196012000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:196006000-196008400	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr3:196006000-196012800	Enhancers	Fetal Intestine Small	intestine
48	chr3:196006000-196013000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr3:196006200-196008600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:196006400-196007800	Enhancers	Primary neutrophils fromperipheralblood	blood

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