Variant report

Variant	rs11150624
Chromosome Location	chr16:31476458-31476459
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	chr16:31475154..31478732-chr16:31483245..31485698,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140682	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1135265	0.82[ASW][hapmap];0.88[CEU][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11643752	0.82[ASW][hapmap];0.81[LWK][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs11646054	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11646911	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12923122	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12930621	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3116150	1.00[ASW][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs35884660	0.80[ASN][1000 genomes]
rs4243237	1.00[JPT][hapmap]
rs4313820	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4482295	0.82[ASW][hapmap];0.82[JPT][hapmap];0.88[LWK][hapmap];0.85[MEX][hapmap]
rs4597343	0.80[ASN][1000 genomes]
rs4889549	0.82[JPT][hapmap]
rs4889661	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[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4889664	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4889666	0.80[ASN][1000 genomes]
rs7201796	0.80[ASN][1000 genomes]
rs7206531	0.80[ASN][1000 genomes]
rs8048218	0.82[ASW][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap]
rs8050563	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs8050712	0.80[ASN][1000 genomes]

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	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
2	nsv833194	chr16:31358179-31528545	Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases
4	nsv905748	chr16:31427678-31559220	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
5	nsv905749	chr16:31427678-31565597	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	96 gene(s)	inside rSNPs	diseases
6	nsv905750	chr16:31427678-31587662	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases
7	nsv905751	chr16:31431360-31489033	Bivalent Enhancer Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
8	nsv905752	chr16:31436932-31565597	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	95 gene(s)	inside rSNPs	diseases
9	nsv905753	chr16:31436932-31587662	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
10	nsv905754	chr16:31451699-31565597	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11150624	TGFB1I1	cis	cerebellum	SCAN
rs11150624	ZNF646	cis	cerebellum	SCAN
rs11150624	FBXL19	cis	cerebellum	SCAN
rs11150624	NCRNA00095	cis	lymphoblastoid	seeQTL
rs11150624	FUS	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31471000-31482600	Weak transcription	Small Intestine	intestine
2	chr16:31471800-31483000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr16:31472000-31478600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr16:31472000-31480400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr16:31472000-31481800	Weak transcription	NHDF-Ad	bronchial
6	chr16:31472000-31482000	Weak transcription	Fetal Heart	heart
7	chr16:31472000-31482400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr16:31472000-31482400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr16:31472000-31482600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr16:31472000-31482600	Weak transcription	Stomach Mucosa	stomach
11	chr16:31472200-31478400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr16:31472600-31476600	Strong transcription	Primary T cells from cord blood	blood
13	chr16:31472600-31478200	Weak transcription	K562	blood
14	chr16:31472600-31479000	Strong transcription	Adipose Nuclei	Adipose
15	chr16:31472600-31479000	Strong transcription	Fetal Intestine Small	intestine
16	chr16:31472600-31482600	Weak transcription	Fetal Brain Male	brain
17	chr16:31472600-31483000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr16:31472800-31477200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr16:31472800-31477600	Strong transcription	HepG2	liver
20	chr16:31472800-31477800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr16:31472800-31478000	Weak transcription	GM12878-XiMat	blood
22	chr16:31472800-31478200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr16:31472800-31478400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr16:31472800-31478800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr16:31472800-31478800	Strong transcription	Esophagus	oesophagus
26	chr16:31472800-31482400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr16:31472800-31482400	Weak transcription	Hela-S3	cervix
28	chr16:31472800-31482400	Weak transcription	HMEC	breast
29	chr16:31472800-31482400	Weak transcription	HSMM	muscle
30	chr16:31473000-31476800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr16:31473000-31477000	Strong transcription	Placenta	Placenta
32	chr16:31473000-31477600	Strong transcription	Fetal Muscle Trunk	muscle
33	chr16:31473000-31478200	Strong transcription	Fetal Muscle Leg	muscle
34	chr16:31473000-31478600	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr16:31473000-31479000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr16:31473000-31479000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr16:31473000-31479000	Strong transcription	Fetal Stomach	stomach
38	chr16:31473200-31476600	Strong transcription	Dnd41	blood
39	chr16:31473200-31477800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr16:31473200-31477800	Strong transcription	Brain Substantia Nigra	brain
41	chr16:31473200-31477800	Strong transcription	Fetal Intestine Large	intestine
42	chr16:31473200-31478000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr16:31473200-31478000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr16:31473200-31478000	Strong transcription	Thymus	Thymus
45	chr16:31473200-31478200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr16:31473200-31478200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr16:31473200-31478400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr16:31473200-31478400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr16:31473200-31478400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr16:31473200-31478400	Strong transcription	Left Ventricle	heart

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