Variant report

Variant	rs11988
Chromosome Location	chr11:47261260-47261261
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47234544..47240299-chr11:47253173..47262641,20	MCF-7	breast:
2	chr11:47257344..47261784-chr11:47428504..47430961,3	K562	blood:
3	chr11:47256660..47261423-chr11:47290143..47292492,5	K562	blood:
4	chr11:47257788..47261523-chr11:47268362..47272495,6	MCF-7	breast:
5	chr11:47260942..47262867-chr11:47285650..47288524,2	MCF-7	breast:
6	chr11:47235763..47239749-chr11:47261118..47265067,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165915	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000134574	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000255197	Chromatin interaction
ENSG00000134575	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10838696	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs11039130	0.82[CHB][hapmap]
rs11039138	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11039139	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039149	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs11039159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039162	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039165	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11039182	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11039183	0.84[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606683	0.84[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2167080	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2596407	1.00[ASN][1000 genomes]
rs2697923	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2856653	1.00[ASN][1000 genomes]
rs7116451	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs749067	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7944419	0.83[ASN][1000 genomes]
rs7944584	0.94[ASN][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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11988	OR4B1	cis	cerebellum	SCAN
rs11988	MADD	cis	parietal	SCAN
rs11988	TP53I11	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47238400-47269400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47240200-47266600	Weak transcription	Fetal Brain Male	brain
3	chr11:47242400-47269200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:47243600-47269200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr11:47246600-47267800	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr11:47247400-47267600	Strong transcription	Thymus	Thymus
7	chr11:47248200-47265200	Strong transcription	GM12878-XiMat	blood
8	chr11:47254000-47264600	Strong transcription	Dnd41	blood
9	chr11:47254600-47267800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr11:47255400-47262000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr11:47255400-47269200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr11:47255600-47264600	Strong transcription	HepG2	liver
13	chr11:47255600-47268800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:47255800-47267600	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr11:47256000-47268000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr11:47256200-47267800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr11:47256400-47267800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr11:47256800-47268800	Strong transcription	Fetal Thymus	thymus
19	chr11:47257000-47261400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:47257400-47262000	Strong transcription	HMEC	breast
21	chr11:47257800-47267800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:47257800-47268000	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr11:47258000-47262600	Strong transcription	HSMMtube	muscle
24	chr11:47258000-47269000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:47258200-47263600	Strong transcription	NHLF	lung
26	chr11:47258200-47267600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr11:47258400-47263200	Strong transcription	Osteobl	bone
28	chr11:47258400-47266400	Strong transcription	Fetal Intestine Large	intestine
29	chr11:47258400-47267800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:47258400-47268400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:47258600-47262400	Strong transcription	NHDF-Ad	bronchial
32	chr11:47258600-47265200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:47258600-47267800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr11:47258600-47267800	Strong transcription	Rectal Smooth Muscle	rectum
35	chr11:47258600-47268800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr11:47258800-47261800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr11:47258800-47264400	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr11:47258800-47267400	Strong transcription	Colon Smooth Muscle	Colon
39	chr11:47258800-47268000	Strong transcription	NHEK	skin
40	chr11:47259000-47264200	Strong transcription	HUVEC	blood vessel
41	chr11:47259000-47268200	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr11:47259000-47268800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr11:47259000-47269000	Strong transcription	Fetal Stomach	stomach
44	chr11:47259200-47262000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr11:47259200-47264000	Strong transcription	Lung	lung
46	chr11:47259200-47268000	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr11:47259400-47261400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr11:47259400-47262000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr11:47259400-47262000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr11:47259400-47263400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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