Variant report

Variant	rs2293576
Chromosome Location	chr11:47434986-47434987
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:47434898-47435470	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:47434770-47441206	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr11:47434885-47438469	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:47202498..47205214-chr11:47434945..47437570,2	K562	blood:
2	chr11:47391440..47404809-chr11:47427075..47436409,23	K562	blood:
3	chr11:47236484..47238469-chr11:47432322..47435260,2	MCF-7	breast:

Variant related genes	Relation type
SLC39A13	TF binding region
ENSG00000255197	TF binding region
ENSG00000134574	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000066336	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10742802	1.00[ASN][1000 genomes]
rs10742814	0.93[GIH][hapmap];0.95[JPT][hapmap]
rs10769263	0.85[ASN][1000 genomes]
rs10769264	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10838702	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.83[ASN][1000 genomes]
rs10838703	1.00[ASW][hapmap];0.92[CEU][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10838705	0.98[ASN][1000 genomes]
rs10838709	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[ASN][1000 genomes]
rs10838726	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10838732	0.95[JPT][hapmap]
rs11039221	0.98[ASN][1000 genomes]
rs11039225	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[ASN][1000 genomes]
rs11039244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039266	1.00[ASW][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap]
rs11039280	1.00[JPT][hapmap]
rs11039290	0.87[CEU][hapmap]
rs12292911	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[ASN][1000 genomes]
rs12361415	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap]
rs12422023	1.00[LWK][hapmap]
rs12577643	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1377416	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.84[ASN][1000 genomes]
rs1534576	0.84[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]
rs2203712	0.95[JPT][hapmap]
rs2242081	0.93[GIH][hapmap];0.95[JPT][hapmap]
rs2280231	1.00[ASW][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap]
rs2293579	0.97[ASN][1000 genomes]
rs3740689	0.83[CHB][hapmap]
rs3740699	0.93[GIH][hapmap];0.84[JPT][hapmap]
rs4434960	0.89[ASN][1000 genomes]
rs61897431	0.97[ASN][1000 genomes]
rs6485758	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs6485763	0.93[GIH][hapmap];0.95[JPT][hapmap]
rs7103648	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7103835	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs7104036	0.91[ASN][1000 genomes]
rs7933019	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs7947450	0.98[ASN][1000 genomes]
rs7950696	0.95[JPT][hapmap]
rs874896	0.84[CEU][hapmap];0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs896817	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[GIH][hapmap];0.80[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv541034	chr11:47404083-47440081	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
9	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
10	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2293576	MADD	cis	parietal	SCAN
rs2293576	C1QTNF4	cis	lymphoblastoid	seeQTL
rs2293576	MYBPC3	cis	multi-tissue	Pritchard
rs2293576	C1QTNF4	cis	multi-tissue	Pritchard
rs2293576	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs2293576	SPI1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47431000-47435000	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr11:47431000-47435400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr11:47431000-47435400	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr11:47431000-47439200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:47431000-47440000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr11:47431000-47442000	Weak transcription	Primary B cells from cord blood	blood
7	chr11:47431200-47435000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr11:47431200-47435200	Weak transcription	Primary T cells from cord blood	blood
9	chr11:47431200-47435400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr11:47431200-47435400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr11:47431200-47435600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr11:47431200-47437600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:47431200-47439000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr11:47431200-47439800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr11:47431200-47440600	Weak transcription	Small Intestine	intestine
16	chr11:47431200-47447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr11:47431400-47435000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr11:47431400-47435000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr11:47431400-47435200	Weak transcription	Liver	Liver
20	chr11:47431400-47436600	Weak transcription	Psoas Muscle	Psoas
21	chr11:47431400-47440400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr11:47431600-47435000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:47431600-47435000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr11:47431600-47435400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr11:47431600-47437400	Strong transcription	Fetal Intestine Small	intestine
26	chr11:47431600-47437800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:47431600-47439000	Weak transcription	K562	blood
28	chr11:47431600-47439600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr11:47431600-47439800	Weak transcription	GM12878-XiMat	blood
30	chr11:47431600-47440200	Genic enhancers	Right Ventricle	heart
31	chr11:47431600-47440400	Weak transcription	Fetal Kidney	kidney
32	chr11:47431600-47446400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr11:47431800-47435200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr11:47431800-47437000	Weak transcription	Right Atrium	heart
35	chr11:47431800-47438800	Genic enhancers	Fetal Muscle Leg	muscle
36	chr11:47431800-47440400	Genic enhancers	Placenta	Placenta
37	chr11:47431800-47440800	Genic enhancers	Fetal Muscle Trunk	muscle
38	chr11:47432000-47437200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr11:47432000-47437400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr11:47432200-47435000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr11:47432200-47435000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr11:47432200-47435000	Weak transcription	Adipose Nuclei	Adipose
43	chr11:47432200-47435000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr11:47432200-47435800	Weak transcription	Fetal Heart	heart
45	chr11:47432200-47436200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr11:47432200-47437200	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr11:47432200-47438600	Genic enhancers	HMEC	breast
48	chr11:47432200-47446400	Strong transcription	Thymus	Thymus
49	chr11:47432400-47435200	Weak transcription	HepG2	liver
50	chr11:47432400-47435400	Strong transcription	Fetal Stomach	stomach

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