Variant report

Variant	rs11033042
Chromosome Location	chr11:35264381-35264382
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:35258928..35261277-chr11:35264057..35266573,2	K562	blood:
2	chr11:35253382..35256369-chr11:35263187..35265388,2	K562	blood:
3	chr11:35262350..35264574-chr11:35271788..35273676,2	MCF-7	breast:
4	chr11:35253382..35256689-chr11:35262779..35266276,3	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10488813	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10836347	0.86[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs10836349	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10836352	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10836353	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10836358	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11033031	0.86[CEU][hapmap];0.87[GIH][hapmap];0.89[EUR][1000 genomes]
rs11033034	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11033039	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11033041	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11033043	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12360706	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12364027	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12575005	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1570216	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3812778	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3829280	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4503504	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4508184	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55715534	0.81[EUR][1000 genomes]
rs56193087	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67384276	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7104662	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7122374	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72638195	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72916162	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	nsv972895	chr11:35259840-35266507	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv975098	chr11:35261190-35266507	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11033042	RAG2	cis	cerebellum	SCAN
rs11033042	CD44	cis	lymphoblastoid	seeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35255400-35266800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr11:35258400-35267400	Weak transcription	Aorta	Aorta
3	chr11:35258400-35269000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:35258800-35267400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr11:35259200-35270200	Weak transcription	Stomach Mucosa	stomach
6	chr11:35260800-35270200	Weak transcription	Fetal Lung	lung
7	chr11:35262600-35269800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:35262600-35270600	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr11:35262800-35264400	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr11:35263000-35264800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr11:35263000-35265000	Enhancers	HSMM	muscle
12	chr11:35263000-35265400	Enhancers	Primary T cells fromperipheralblood	blood
13	chr11:35263000-35266400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr11:35263000-35270000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr11:35263000-35270000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr11:35263000-35270200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr11:35263000-35270200	Weak transcription	Fetal Brain Male	brain
18	chr11:35263400-35264400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:35263400-35264800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr11:35263400-35264800	Weak transcription	Pancreas	Pancrea
21	chr11:35263400-35264800	Enhancers	Osteobl	bone
22	chr11:35263400-35265600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr11:35263400-35265800	Enhancers	Primary T cells from cord blood	blood
24	chr11:35263400-35270600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr11:35263600-35264800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr11:35263600-35270000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr11:35263800-35264600	Enhancers	HSMMtube	muscle
28	chr11:35263800-35264600	Enhancers	NH-A	brain
29	chr11:35263800-35265400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr11:35264000-35264400	Enhancers	Colon Smooth Muscle	Colon
31	chr11:35264000-35264400	Enhancers	NHLF	lung
32	chr11:35264000-35264600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:35264000-35264600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr11:35264000-35264600	Enhancers	NHDF-Ad	bronchial
35	chr11:35264000-35267200	Weak transcription	Rectal Smooth Muscle	rectum

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