Variant report

Variant	rs10836347
Chromosome Location	chr11:35253133-35253134
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10128586	0.81[CEU][hapmap]
rs10488813	0.96[EUR][1000 genomes]
rs10836343	0.81[CEU][hapmap]
rs10836349	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10836352	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10836353	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10836358	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11033029	0.83[EUR][1000 genomes]
rs11033031	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11033033	0.81[AMR][1000 genomes]
rs11033034	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11033039	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11033041	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11033042	0.96[EUR][1000 genomes]
rs11033043	0.96[EUR][1000 genomes]
rs12360706	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs12364027	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12575005	0.96[EUR][1000 genomes]
rs1570216	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs3812778	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.83[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs3829280	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs4503504	0.94[EUR][1000 genomes]
rs4508184	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs55715534	0.86[EUR][1000 genomes]
rs56193087	0.97[EUR][1000 genomes]
rs67384276	0.97[EUR][1000 genomes]
rs7104662	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7122374	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs72638195	0.96[EUR][1000 genomes]
rs72916162	0.86[EUR][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	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv541003	chr11:35122694-35261451	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv541004	chr11:35122694-35297414	Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv897216	chr11:35241989-35255821	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv897217	chr11:35241989-35257316	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv897218	chr11:35241989-35261374	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv897219	chr11:35242907-35257316	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv897220	chr11:35242907-35261374	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
9	nsv897221	chr11:35242907-35265444	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
10	nsv897222	chr11:35244044-35261374	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10836347	RAG2	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35233400-35259600	Weak transcription	Liver	Liver
2	chr11:35236200-35254400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr11:35236400-35253400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:35236400-35253400	Strong transcription	Fetal Muscle Trunk	muscle
5	chr11:35236800-35253200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr11:35236800-35259600	Weak transcription	Psoas Muscle	Psoas
7	chr11:35237000-35254600	Strong transcription	HSMM	muscle
8	chr11:35237000-35259600	Weak transcription	HUVEC	blood vessel
9	chr11:35238800-35253200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:35239200-35253200	Strong transcription	NHEK	skin
11	chr11:35239200-35253600	Strong transcription	HMEC	breast
12	chr11:35239200-35257600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:35239400-35253800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr11:35239800-35254600	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr11:35239800-35254600	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr11:35239800-35255000	Strong transcription	Primary T cells from cord blood	blood
17	chr11:35240200-35253200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr11:35240200-35253800	Strong transcription	Duodenum Mucosa	Duodenum
19	chr11:35240200-35254000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr11:35240400-35253400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
21	chr11:35240600-35253800	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr11:35240600-35254000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr11:35240600-35254400	Strong transcription	NH-A	brain
24	chr11:35240800-35254600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr11:35241000-35253800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:35241200-35253800	Strong transcription	Osteobl	bone
27	chr11:35241200-35259600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr11:35243200-35254400	Strong transcription	A549	lung
29	chr11:35243600-35258200	Weak transcription	GM12878-XiMat	blood
30	chr11:35245200-35253200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:35245400-35259600	Weak transcription	Brain Hippocampus Middle	brain
32	chr11:35245800-35255400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr11:35245800-35256600	Weak transcription	Small Intestine	intestine
34	chr11:35246000-35253400	Strong transcription	Fetal Muscle Leg	muscle
35	chr11:35246600-35254800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr11:35247000-35258000	Weak transcription	Colonic Mucosa	Colon
37	chr11:35247000-35263200	Weak transcription	HSMMtube	muscle
38	chr11:35247200-35257600	Weak transcription	Thymus	Thymus
39	chr11:35248400-35253400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr11:35248600-35253200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:35248800-35253800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr11:35249400-35253200	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr11:35249400-35253400	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr11:35249400-35253600	Strong transcription	Primary hematopoietic stem cells	blood
45	chr11:35249400-35254800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:35249600-35253600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr11:35249800-35253200	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr11:35249800-35253400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr11:35249800-35254200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr11:35249800-35254200	Strong transcription	Primary T helper cells PMA-I stimulated	--

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