Variant report

Variant	rs10742300
Chromosome Location	chr11:33668284-33668285
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1033542	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1033543	1.00[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1073655	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10742298	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10742299	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10742301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10768013	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10836087	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10836088	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1569763	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4755237	0.82[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4755765	0.83[MEX][hapmap]
rs4755771	0.87[MEX][hapmap]
rs7106651	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7115033	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7117579	1.00[ASW][hapmap];0.82[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs768474	1.00[ASW][hapmap];0.87[MEX][hapmap]
rs7949170	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832112	chr11:33469782-33683052	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10742300	C11orf41	cis	cerebellum	SCAN
rs10742300	PAMR1	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:33640800-33673600	Weak transcription	Fetal Brain Male	brain
2	chr11:33642600-33673600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr11:33643000-33673600	Weak transcription	Brain Angular Gyrus	brain
4	chr11:33656800-33673600	Weak transcription	NH-A	brain
5	chr11:33657400-33673600	Weak transcription	HSMMtube	muscle
6	chr11:33657800-33673600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr11:33657800-33688400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr11:33662800-33668600	Weak transcription	Right Atrium	heart
9	chr11:33663400-33673600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr11:33664800-33670200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:33665400-33673000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr11:33665400-33673200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:33665600-33673400	Weak transcription	HSMM	muscle
14	chr11:33665800-33691600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr11:33666400-33668400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr11:33666400-33668800	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr11:33666400-33668800	Strong transcription	Brain Germinal Matrix	brain
18	chr11:33666600-33668400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr11:33666600-33673000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:33666800-33668800	Enhancers	Adipose Nuclei	Adipose
21	chr11:33666800-33677200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:33667600-33668800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr11:33667600-33668800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr11:33667600-33668800	Enhancers	HUVEC	blood vessel
25	chr11:33667600-33673200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr11:33667600-33679400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr11:33668000-33668800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr11:33668000-33676800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr11:33668000-33677400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr11:33668200-33668400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr11:33668200-33672000	Weak transcription	Fetal Brain Female	brain
32	chr11:33668200-33673200	Weak transcription	Left Ventricle	heart

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