Variant report

Variant	rs12361673
Chromosome Location	chr11:46723937-46723938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:46639444..46641700-chr11:46721393..46724232,2	K562	blood:
2	chr11:46722213..46727380-chr11:46743173..46747634,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180210	Chromatin interaction
ENSG00000180423	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1007738	0.89[GIH][hapmap]
rs10734548	0.86[GIH][hapmap]
rs10769205	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10769211	0.89[GIH][hapmap]
rs11039014	0.89[GIH][hapmap]
rs11606709	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12274785	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13448	0.88[CEU][hapmap];0.97[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs1551744	0.89[GIH][hapmap]
rs2070852	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.80[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2282686	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2306029	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2306032	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3136505	0.83[EUR][1000 genomes]
rs4606447	1.00[ASW][hapmap];0.94[CEU][hapmap];0.97[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4752926	0.84[CHD][hapmap]
rs4752929	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57804402	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6485696	0.82[CHB][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.83[TSI][hapmap]
rs6485702	0.82[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs7101374	0.89[GIH][hapmap]
rs7107778	0.86[GIH][hapmap]
rs7929294	0.86[GIH][hapmap]
rs7932354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs964551	0.86[GIH][hapmap]
rs9704782	0.86[EUR][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	nsv1044225	chr11:46472580-46771102	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv541030	chr11:46472580-46771102	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats 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 miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12361673	C11orf49	cis	parietal	SCAN
rs12361673	DKFZp779M0652	cis	parietal	SCAN
rs12361673	ACP2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46721200-46724000	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr11:46723200-46724000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr11:46723200-46724000	Active TSS	HepG2	liver
4	chr11:46723200-46724400	Weak transcription	Aorta	Aorta
5	chr11:46723400-46724000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr11:46723400-46724000	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr11:46723400-46724000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:46723400-46724000	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr11:46723400-46724000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr11:46723400-46724000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr11:46723400-46724000	Enhancers	Stomach Mucosa	stomach
12	chr11:46723400-46724200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:46723400-46724200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr11:46723400-46724200	Enhancers	Primary B cells from peripheral blood	blood
15	chr11:46723400-46724200	Weak transcription	Gastric	stomach
16	chr11:46723400-46724200	Weak transcription	Lung	lung
17	chr11:46723400-46724200	Weak transcription	Pancreas	Pancrea
18	chr11:46723400-46724200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr11:46723400-46724200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr11:46723400-46724400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr11:46723400-46724400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr11:46723400-46724400	Weak transcription	Esophagus	oesophagus
23	chr11:46723400-46724400	Weak transcription	Right Ventricle	heart
24	chr11:46723400-46724600	Genic enhancers	Primary B cells from cord blood	blood
25	chr11:46723400-46724600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr11:46723400-46724800	Genic enhancers	Primary T cells fromperipheralblood	blood
27	chr11:46723400-46724800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr11:46723400-46725000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr11:46723400-46727200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr11:46723600-46724000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr11:46723600-46724000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:46723600-46724000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr11:46723600-46724000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr11:46723600-46724000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr11:46723600-46724000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr11:46723600-46724000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr11:46723600-46724000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr11:46723600-46724000	Enhancers	Brain Cingulate Gyrus	brain
39	chr11:46723600-46724000	Enhancers	Colon Smooth Muscle	Colon
40	chr11:46723600-46724000	Weak transcription	Fetal Intestine Large	intestine
41	chr11:46723600-46724000	Genic enhancers	Dnd41	blood
42	chr11:46723600-46724000	Enhancers	GM12878-XiMat	blood
43	chr11:46723600-46724000	Weak transcription	HMEC	breast
44	chr11:46723600-46724000	Weak transcription	HSMMtube	muscle
45	chr11:46723600-46724000	Weak transcription	HUVEC	blood vessel
46	chr11:46723600-46724000	Weak transcription	K562	blood
47	chr11:46723600-46724000	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr11:46723600-46724000	Weak transcription	NH-A	brain
49	chr11:46723600-46724000	Weak transcription	NHDF-Ad	bronchial
50	chr11:46723600-46724200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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