Variant report

Variant	rs3781839
Chromosome Location	chr11:33693548-33693549
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:33689243..33690846-chr11:33691492..33694193,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10836094	0.81[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs10836095	0.81[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.88[ASN][1000 genomes]
rs1096557	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11032332	0.81[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.88[ASN][1000 genomes]
rs11032335	0.81[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11032338	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11601472	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12226271	0.88[ASN][1000 genomes]
rs12280103	0.88[ASN][1000 genomes]
rs12574994	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1321015	0.81[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs1321016	0.81[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2295064	0.81[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.88[ASN][1000 genomes]
rs3741020	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741021	0.93[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101438	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832113	chr11:33609202-33767781	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3781839	C11orf41	Cis_1M	lymphoblastoid	RTeQTL
rs3781839	PRRG4	cis	cerebellum	SCAN
rs3781839	CAT	cis	cerebellum	SCAN
rs3781839	RAG2	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:33674800-33700000	Weak transcription	Brain Angular Gyrus	brain
2	chr11:33678800-33695400	Weak transcription	Brain Anterior Caudate	brain
3	chr11:33685200-33697800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:33689400-33693800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:33689800-33695600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:33690000-33695600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr11:33690400-33693600	Weak transcription	Fetal Brain Female	brain
8	chr11:33690800-33694400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr11:33691000-33693800	Enhancers	NHLF	lung
10	chr11:33691000-33694000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:33691000-33694000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr11:33691000-33695600	Weak transcription	Fetal Muscle Leg	muscle
13	chr11:33691000-33695600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr11:33691000-33701600	Weak transcription	Gastric	stomach
15	chr11:33691000-33712400	Weak transcription	Psoas Muscle	Psoas
16	chr11:33691400-33696800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:33691800-33704200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr11:33692400-33695400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr11:33692600-33695000	Weak transcription	HSMMtube	muscle
20	chr11:33692600-33695200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr11:33692800-33693600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr11:33692800-33695200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:33693000-33695400	Weak transcription	HSMM	muscle
24	chr11:33693000-33695400	Weak transcription	NH-A	brain
25	chr11:33693000-33695400	Weak transcription	NHDF-Ad	bronchial
26	chr11:33693000-33695600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr11:33693000-33695800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr11:33693000-33696400	Weak transcription	HUVEC	blood vessel
29	chr11:33693000-33697000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr11:33693000-33699600	Weak transcription	Brain Germinal Matrix	brain
31	chr11:33693000-33700000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:33693000-33703400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr11:33693200-33693600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr11:33693200-33695000	Weak transcription	Osteobl	bone
35	chr11:33693200-33695400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr11:33693400-33694400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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