Variant report

Variant	rs11604876
Chromosome Location	chr11:46768041-46768042
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:46760225..46762619-chr11:46766210..46768757,2	MCF-7	breast:
2	chr11:46761363..46764873-chr11:46765216..46768275,3	K562	blood:
3	chr11:46763360..46766169-chr11:46766734..46769498,4	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1007738	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10734548	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10769211	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10838612	0.82[CHB][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap]
rs11038977	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11038994	1.00[AFR][1000 genomes]
rs11039002	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes]
rs11039014	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11039035	0.91[MEX][hapmap];0.88[TSI][hapmap]
rs11600292	0.81[MEX][hapmap]
rs11602036	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11602537	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12574512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12575609	0.81[AMR][1000 genomes]
rs1551744	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap]
rs1799867	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2070850	1.00[CEU][hapmap];0.87[CHB][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2070851	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2306028	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs2306033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs2306036	0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs2306037	1.00[JPT][hapmap]
rs3136441	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3136447	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3136449	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3136457	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3136458	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3136460	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3136499	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4076557	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4294527	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4453193	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4453194	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4491174	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4534535	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4581406	0.95[MEX][hapmap]
rs4603265	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4752927	0.89[GIH][hapmap];0.91[JPT][hapmap]
rs4752931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4752932	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[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4752933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4752936	1.00[AFR][1000 genomes]
rs4752940	1.00[AFR][1000 genomes]
rs4752946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs4752947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs57704144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58561056	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58922799	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5896	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61337452	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7101374	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7107778	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7929294	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs7940441	0.82[JPT][hapmap]
rs7940682	0.82[ASN][1000 genomes]
rs964551	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv430382	chr11:46743135-46849360	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	esv3388509	chr11:46763105-46818814	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11604876	DDB2	Cis_1M	lymphoblastoid	RTeQTL
rs11604876	ACP2	cis	lymphoblastoid	seeQTL
rs11604876	PTPMT1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46753000-46786600	Weak transcription	Right Atrium	heart
2	chr11:46760200-46786800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr11:46760200-46794800	Strong transcription	A549	lung
4	chr11:46760400-46777400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr11:46760400-46781400	Weak transcription	Stomach Mucosa	stomach
6	chr11:46760400-46795600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:46760600-46785800	Strong transcription	Fetal Stomach	stomach
8	chr11:46760600-46793800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr11:46761200-46772400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:46761200-46787000	Strong transcription	Fetal Muscle Trunk	muscle
11	chr11:46761200-46787600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr11:46761400-46786600	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr11:46761400-46795800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr11:46761400-46840000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:46761400-46845200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:46761600-46776200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:46761600-46787000	Strong transcription	Fetal Intestine Large	intestine
18	chr11:46761600-46824600	Strong transcription	Fetal Thymus	thymus
19	chr11:46762200-46776200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr11:46762400-46787000	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr11:46762400-46794200	Strong transcription	Adipose Nuclei	Adipose
22	chr11:46762600-46769800	Strong transcription	GM12878-XiMat	blood
23	chr11:46762600-46770000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr11:46762600-46770000	Strong transcription	Primary hematopoietic stem cells	blood
25	chr11:46762600-46770000	Strong transcription	HUVEC	blood vessel
26	chr11:46762600-46770000	Strong transcription	NHDF-Ad	bronchial
27	chr11:46762600-46770000	Strong transcription	Osteobl	bone
28	chr11:46762600-46770200	Strong transcription	HSMMtube	muscle
29	chr11:46762600-46776600	Strong transcription	Brain Germinal Matrix	brain
30	chr11:46762600-46778600	Strong transcription	HSMM	muscle
31	chr11:46762600-46785600	Strong transcription	Thymus	Thymus
32	chr11:46762600-46786400	Strong transcription	Fetal Brain Female	brain
33	chr11:46762600-46786600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr11:46762600-46786800	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr11:46762600-46786800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr11:46762600-46787000	Strong transcription	Fetal Muscle Leg	muscle
37	chr11:46762600-46793200	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr11:46762600-46794800	Strong transcription	Placenta	Placenta
39	chr11:46762600-46795200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:46762600-46795200	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr11:46762600-46795800	Strong transcription	Dnd41	blood
42	chr11:46762600-46804000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr11:46762600-46826000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr11:46762600-46841400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr11:46762800-46768800	Strong transcription	K562	blood
46	chr11:46762800-46770000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr11:46762800-46770000	Strong transcription	Brain Angular Gyrus	brain
48	chr11:46762800-46770000	Strong transcription	Brain Cingulate Gyrus	brain
49	chr11:46762800-46770000	Strong transcription	Brain Hippocampus Middle	brain
50	chr11:46762800-46770200	Strong transcription	Gastric	stomach

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