Variant report

Variant	rs1809087
Chromosome Location	chr2:46793301-46793302
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46787456..46790451-chr2:46790520..46794497,4	K562	blood:
2	chr2:46787456..46790384-chr2:46790520..46794497,4	K562	blood:
3	chr2:46773973..46776728-chr2:46790942..46793307,2	MCF-7	breast:
4	chr2:46790452..46793427-chr2:46811827..46814978,3	MCF-7	breast:
5	chr2:46781985..46785151-chr2:46792596..46794911,4	MCF-7	breast:
6	chr2:46768824..46771008-chr2:46791794..46793786,2	K562	blood:

Variant related genes	Relation type
ENSG00000250565	Chromatin interaction
ENSG00000119729	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1057899	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1060656	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11306	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1137748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11901678	0.87[ASN][1000 genomes]
rs11903907	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13404342	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13406609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13410076	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1376406	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1456018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17035272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035361	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2276554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3213985	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3768723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3768725	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4300884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4377377	0.87[ASN][1000 genomes]
rs57134465	0.87[ASN][1000 genomes]
rs57955462	0.87[ASN][1000 genomes]
rs58101879	0.87[ASN][1000 genomes]
rs58342271	0.81[ASN][1000 genomes]
rs59183773	0.87[ASN][1000 genomes]
rs59823825	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60199254	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60211996	0.87[ASN][1000 genomes]
rs60738814	0.81[ASN][1000 genomes]
rs61252474	0.87[ASN][1000 genomes]
rs6544904	0.87[ASN][1000 genomes]
rs6713104	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6719813	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6727471	0.87[ASN][1000 genomes]
rs6733143	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6749372	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6756134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs68104662	0.86[ASN][1000 genomes]
rs72875696	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7589908	0.87[ASN][1000 genomes]
rs7591561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7592446	0.81[ASN][1000 genomes]
rs962467	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808496	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription 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	36 gene(s)	inside rSNPs	diseases
5	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats 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 target site	31 gene(s)	inside rSNPs	diseases
6	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1809087	RHOQ	cis	multi-tissue	Pritchard

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46771200-46812800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:46771400-46796000	Weak transcription	Fetal Kidney	kidney
3	chr2:46771800-46795600	Weak transcription	Fetal Brain Male	brain
4	chr2:46772200-46804000	Weak transcription	NH-A	brain
5	chr2:46773200-46806000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr2:46775600-46815800	Weak transcription	Fetal Brain Female	brain
7	chr2:46776800-46794600	Weak transcription	Ovary	ovary
8	chr2:46779800-46794600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr2:46782200-46798400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:46782400-46806600	Weak transcription	Brain Germinal Matrix	brain
11	chr2:46782800-46803600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:46783000-46795600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:46783000-46796800	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:46783000-46807200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:46783200-46795400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:46783200-46803000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr2:46783600-46838000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:46784000-46802800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr2:46785400-46796000	Weak transcription	HSMM	muscle
20	chr2:46785400-46798400	Weak transcription	Liver	Liver
21	chr2:46785400-46807600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:46785400-46809400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr2:46785600-46796400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:46785600-46803800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:46786600-46795000	Strong transcription	Fetal Stomach	stomach
26	chr2:46786800-46805200	Weak transcription	Small Intestine	intestine
27	chr2:46787200-46799800	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr2:46787800-46806600	Weak transcription	Gastric	stomach
29	chr2:46788400-46793400	Enhancers	Duodenum Mucosa	Duodenum
30	chr2:46789400-46795400	Weak transcription	Fetal Intestine Small	intestine
31	chr2:46789400-46811200	Weak transcription	Colonic Mucosa	Colon
32	chr2:46789600-46796400	Weak transcription	Pancreas	Pancrea
33	chr2:46789800-46796600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:46789800-46805800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr2:46789800-46807000	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr2:46790000-46803400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:46790000-46803800	Weak transcription	Primary T cells from cord blood	blood
38	chr2:46790000-46807200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:46790000-46842000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:46790200-46803400	Weak transcription	A549	lung
41	chr2:46790200-46807000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr2:46790200-46807400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:46790600-46795600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:46790600-46795600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr2:46790600-46803800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:46790600-46806200	Weak transcription	Dnd41	blood
47	chr2:46790800-46795000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:46791000-46794000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:46791000-46795200	Genic enhancers	Primary monocytes fromperipheralblood	blood
50	chr2:46791000-46795400	Enhancers	Left Ventricle	heart

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