Variant report

Variant	rs999295
Chromosome Location	chr11:5730248-5730249
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	11:5033143-5038367..11:5721056-5732713	GM12878	blood:
2	11:4957178-4961904..11:5721056-5732713	H1-hESC	embryonic stem cell:	embryo
3	11:4988858-5002113..11:5721056-5732713	Hela-S3	cervix:
4	11:5087036-5092291..11:5721056-5732713	K562	blood:
5	11:5488942-5494633..11:5721056-5732713	H1-hESC	embryonic stem cell:	embryo
6	11:5586716-5591774..11:5721056-5732713	GM12878	blood:

Variant related genes	Relation type
ENSG00000227023	Chromatin interaction
ENSG00000230484	Chromatin interaction
ENSG00000225003	Chromatin interaction
ENSG00000224300	Chromatin interaction
ENSG00000233646	Chromatin interaction
ENSG00000273085	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10769197	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10838568	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10838583	0.93[AMR][1000 genomes]
rs11038886	0.89[MEX][hapmap]
rs12287535	1.00[CEU][hapmap];0.86[GIH][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs1498550	0.89[MEX][hapmap]
rs1498561	0.81[AMR][1000 genomes]
rs2133265	0.89[MEX][hapmap]
rs2343233	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4910841	0.94[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910842	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4910843	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7113258	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs7116081	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7120306	0.89[MEX][hapmap]
rs7131278	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7397032	0.89[MEX][hapmap]
rs7479906	0.84[MEX][hapmap]
rs7932541	0.84[MEX][hapmap]
rs7948996	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9971462	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9971583	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv896939	chr11:5497799-5809548	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv1041568	chr11:5585716-5765688	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1053414	chr11:5612989-6030212	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv553273	chr11:5639873-5871831	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv1036389	chr11:5695451-6177680	Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
9	nsv540943	chr11:5695451-6177680	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
10	nsv553277	chr11:5722948-6010075	Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs999295	C11orf42	cis	cerebellum	SCAN
rs999295	OR51F1	cis	cerebellum	SCAN
rs999295	PHLDA2	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5712400-5730600	Weak transcription	Fetal Lung	lung
2	chr11:5712400-5731800	Weak transcription	NH-A	brain
3	chr11:5712400-5732400	Weak transcription	Pancreas	Pancrea
4	chr11:5712400-5732400	Weak transcription	Stomach Mucosa	stomach
5	chr11:5712600-5732000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr11:5712600-5732600	Weak transcription	Colonic Mucosa	Colon
7	chr11:5713000-5734600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr11:5713600-5730800	Weak transcription	Brain Anterior Caudate	brain
9	chr11:5713600-5734800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:5713600-5745800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:5713800-5731200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr11:5714000-5732600	Weak transcription	Brain Substantia Nigra	brain
13	chr11:5715200-5733000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:5717400-5732400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr11:5717400-5734400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr11:5717600-5731200	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr11:5717600-5732600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:5718000-5734600	Weak transcription	HUVEC	blood vessel
19	chr11:5720000-5732600	Weak transcription	Brain Hippocampus Middle	brain
20	chr11:5720200-5730600	Weak transcription	Placenta	Placenta
21	chr11:5720200-5731800	Weak transcription	Small Intestine	intestine
22	chr11:5720200-5731800	Weak transcription	NHLF	lung
23	chr11:5720200-5732600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr11:5720400-5732800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr11:5720600-5731200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr11:5722000-5730400	Strong transcription	NHDF-Ad	bronchial
27	chr11:5722000-5732800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:5722600-5732600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr11:5722600-5733000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr11:5722800-5731200	Strong transcription	Primary B cells from cord blood	blood
31	chr11:5723000-5731800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr11:5723000-5733000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr11:5723200-5730800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr11:5723400-5731600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr11:5723400-5733800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr11:5723600-5731200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr11:5723600-5731200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr11:5723800-5731200	Strong transcription	Adipose Nuclei	Adipose
39	chr11:5723800-5733000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr11:5724000-5731200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr11:5724400-5732400	Strong transcription	Primary T cells from cord blood	blood
42	chr11:5725400-5730600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:5725400-5732800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr11:5725400-5733600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:5726200-5732600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr11:5726400-5731200	Strong transcription	Osteobl	bone
47	chr11:5726600-5731400	Strong transcription	Fetal Thymus	thymus
48	chr11:5726600-5732400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr11:5726800-5731200	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr11:5726800-5731800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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