Variant report

Variant	rs12099036
Chromosome Location	chr11:5732617-5732618
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	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
ENSG00000230484	Chromatin interaction
ENSG00000227023	Chromatin interaction
ENSG00000273085	Chromatin interaction
ENSG00000225003	Chromatin interaction
ENSG00000224300	Chromatin interaction
ENSG00000233646	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10400251	0.94[ASN][1000 genomes]
rs10742781	0.82[EUR][1000 genomes]
rs10769202	0.81[EUR][1000 genomes]
rs11038865	0.89[EUR][1000 genomes]
rs11038881	0.89[EUR][1000 genomes]
rs11038884	0.82[EUR][1000 genomes]
rs11038885	0.82[EUR][1000 genomes]
rs11038886	0.94[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs11603678	0.82[EUR][1000 genomes]
rs12224409	0.89[EUR][1000 genomes]
rs12792180	0.94[ASN][1000 genomes]
rs12792550	0.96[ASN][1000 genomes]
rs12800896	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12803433	0.94[ASN][1000 genomes]
rs12805134	0.94[ASN][1000 genomes]
rs1498550	0.94[CEU][hapmap];0.90[TSI][hapmap]
rs1498551	0.82[EUR][1000 genomes]
rs1498560	0.83[EUR][1000 genomes]
rs1498561	0.91[EUR][1000 genomes]
rs1532516	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs1603796	0.94[ASN][1000 genomes]
rs2133265	0.87[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs2133267	0.81[EUR][1000 genomes]
rs34279421	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34464178	0.97[ASN][1000 genomes]
rs34559010	0.94[ASN][1000 genomes]
rs34624600	0.97[ASN][1000 genomes]
rs34734399	0.89[ASN][1000 genomes]
rs34772298	0.94[ASN][1000 genomes]
rs34818142	1.00[ASN][1000 genomes]
rs35257755	1.00[ASN][1000 genomes]
rs35378018	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35476279	0.99[ASN][1000 genomes]
rs35725436	0.97[ASN][1000 genomes]
rs36092957	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36173363	0.93[ASN][1000 genomes]
rs4457786	0.94[ASN][1000 genomes]
rs4573706	0.94[ASN][1000 genomes]
rs57610338	0.83[EUR][1000 genomes]
rs57677974	0.89[EUR][1000 genomes]
rs6578681	0.80[EUR][1000 genomes]
rs66481907	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67573252	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7120306	0.94[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs7128460	0.93[CEU][hapmap];0.84[CHB][hapmap];0.89[EUR][1000 genomes]
rs7130646	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71490147	1.00[ASN][1000 genomes]
rs71490148	1.00[ASN][1000 genomes]
rs73404203	0.88[AFR][1000 genomes]
rs73404206	0.89[AFR][1000 genomes]
rs73404207	0.91[AFR][1000 genomes]
rs73404224	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7396310	0.82[EUR][1000 genomes]
rs7397032	0.87[CEU][hapmap];0.90[TSI][hapmap]
rs7479906	0.87[CEU][hapmap]
rs7482494	0.82[EUR][1000 genomes]
rs7482656	0.82[EUR][1000 genomes]
rs7925088	0.89[EUR][1000 genomes]
rs7930210	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7932541	0.94[CEU][hapmap];0.83[TSI][hapmap]
rs7936441	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7937241	0.94[ASN][1000 genomes]
rs7949329	0.88[EUR][1000 genomes]
rs7951137	0.87[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
11	esv1843296	chr11:5730377-5970717	Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
12	esv2758255	chr11:5730377-5970717	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
13	esv2759801	chr11:5730377-6007613	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12099036	TRIM68	cis	cerebellum	SCAN
rs12099036	C11orf17	cis	parietal	SCAN
rs12099036	SMPD1	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5713000-5734600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr11:5713600-5734800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:5713600-5745800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr11:5715200-5733000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr11:5717400-5734400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:5718000-5734600	Weak transcription	HUVEC	blood vessel
7	chr11:5720400-5732800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr11:5722000-5732800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr11:5722600-5733000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr11:5723000-5733000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr11:5723400-5733800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr11:5723800-5733000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:5725400-5732800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr11:5725400-5733600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr11:5727200-5732800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:5727400-5732800	Strong transcription	HSMM	muscle
17	chr11:5727600-5732800	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr11:5729800-5733000	Strong transcription	GM12878-XiMat	blood
19	chr11:5730400-5733600	Weak transcription	NHDF-Ad	bronchial
20	chr11:5730400-5736000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr11:5730800-5733600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr11:5731000-5733600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:5731000-5734000	Weak transcription	Fetal Muscle Leg	muscle
24	chr11:5731000-5734200	Weak transcription	Colon Smooth Muscle	Colon
25	chr11:5731000-5741000	Weak transcription	HSMMtube	muscle
26	chr11:5731000-5743800	Weak transcription	Liver	Liver
27	chr11:5731200-5732800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr11:5731200-5732800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr11:5731200-5732800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr11:5731200-5732800	Weak transcription	Thymus	Thymus
31	chr11:5731200-5733000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:5731200-5733200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr11:5731200-5733400	Weak transcription	Left Ventricle	heart
34	chr11:5731200-5734200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr11:5731200-5734600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr11:5731200-5734800	Weak transcription	Lung	lung
37	chr11:5731200-5735200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:5731200-5736400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr11:5731200-5740600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr11:5731200-5740600	Weak transcription	Primary B cells from cord blood	blood
41	chr11:5731200-5740600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr11:5731200-5740600	Weak transcription	Adipose Nuclei	Adipose
43	chr11:5731200-5741000	Weak transcription	Osteobl	bone
44	chr11:5731200-5748000	Weak transcription	Spleen	Spleen
45	chr11:5731200-5748200	Weak transcription	Placenta	Placenta
46	chr11:5731200-5749200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr11:5731400-5733000	Weak transcription	Fetal Thymus	thymus
48	chr11:5731400-5733200	Weak transcription	Dnd41	blood
49	chr11:5731400-5733800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr11:5731400-5735400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links