Variant report

Variant	rs2293579
Chromosome Location	chr11:47440758-47440759
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	chr11:47439065..47440854-chr11:47490172..47492482,2	K562	blood:
2	chr11:47439354..47441139-chr11:47490982..47492763,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10437655	0.91[EUR][1000 genomes]
rs10742802	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10742814	0.95[JPT][hapmap]
rs10769263	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10769264	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10838702	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10838705	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10838709	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10838726	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs10838732	0.95[JPT][hapmap]
rs11039221	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039225	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039244	0.84[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs11039280	1.00[JPT][hapmap]
rs11606287	0.92[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs12292911	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12577643	0.90[ASN][1000 genomes]
rs1377416	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1534576	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2203712	0.95[JPT][hapmap]
rs2242081	0.95[JPT][hapmap]
rs2278890	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2293576	0.84[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[ASN][1000 genomes]
rs35032070	0.85[EUR][1000 genomes]
rs3740699	0.84[JPT][hapmap]
rs3758675	0.82[EUR][1000 genomes]
rs3824869	0.88[CEU][hapmap]
rs4434960	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61897431	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6485758	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6485763	0.95[JPT][hapmap]
rs7103648	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7104036	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7933019	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7947450	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7950696	0.95[JPT][hapmap]
rs874896	1.00[CEU][hapmap];0.87[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs896817	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv825871	chr11:47376020-47457537	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv554210	chr11:47380593-47449544	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
8	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
9	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Serum albumin level	23022100	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2293579	C1QTNF4	cis	multi-tissue	Pritchard
rs2293579		cis	Lymphoblastoid	GTEx
rs2293579	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs2293579	MADD	cis	parietal	SCAN
rs2293579	C1QTNF4	cis	lymphoblastoid	seeQTL
rs2293579	MTCH2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47431000-47442000	Weak transcription	Primary B cells from cord blood	blood
2	chr11:47431200-47447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:47431600-47446400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr11:47431800-47440800	Genic enhancers	Fetal Muscle Trunk	muscle
5	chr11:47432200-47446400	Strong transcription	Thymus	Thymus
6	chr11:47432400-47440800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr11:47432400-47445800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr11:47432400-47446400	Weak transcription	Fetal Brain Male	brain
9	chr11:47432600-47445800	Strong transcription	Brain Anterior Caudate	brain
10	chr11:47432600-47446400	Strong transcription	Fetal Brain Female	brain
11	chr11:47432800-47446000	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr11:47432800-47446200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr11:47432800-47446400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr11:47433200-47446200	Strong transcription	Fetal Thymus	thymus
15	chr11:47433400-47445800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr11:47434200-47445600	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr11:47434800-47446000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:47435000-47440800	Genic enhancers	NHLF	lung
19	chr11:47435000-47446000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr11:47435000-47446200	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr11:47435000-47446200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr11:47435000-47446600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr11:47435200-47445800	Strong transcription	Liver	Liver
24	chr11:47435200-47446000	Strong transcription	Primary B cells from peripheral blood	blood
25	chr11:47435200-47446400	Strong transcription	Primary T cells from cord blood	blood
26	chr11:47436000-47441000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr11:47437400-47446400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:47437800-47446600	Strong transcription	Fetal Intestine Large	intestine
29	chr11:47438000-47445600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr11:47438000-47446200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr11:47438000-47446200	Strong transcription	Fetal Intestine Small	intestine
32	chr11:47438200-47441600	Weak transcription	Stomach Mucosa	stomach
33	chr11:47438200-47444200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr11:47438200-47446000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr11:47438200-47446000	Strong transcription	Adipose Nuclei	Adipose
36	chr11:47438200-47446200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr11:47438200-47446400	Weak transcription	Right Atrium	heart
38	chr11:47438200-47446600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr11:47438400-47445400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr11:47438400-47445800	Strong transcription	Fetal Stomach	stomach
41	chr11:47438400-47446000	Strong transcription	NHDF-Ad	bronchial
42	chr11:47438400-47446200	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr11:47438600-47446000	Strong transcription	Brain Cingulate Gyrus	brain
44	chr11:47438600-47446000	Strong transcription	NHEK	skin
45	chr11:47438600-47446200	Strong transcription	Brain Germinal Matrix	brain
46	chr11:47438800-47444200	Strong transcription	Dnd41	blood
47	chr11:47438800-47445800	Strong transcription	Fetal Muscle Leg	muscle
48	chr11:47438800-47446000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr11:47438800-47446400	Strong transcription	Fetal Lung	lung
50	chr11:47439000-47441800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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