Variant report

Variant	rs10916266
Chromosome Location	chr1:228303048-228303049
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MRPL55-1	chr1:228302157-228303181	NONHSAT009976

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10127705	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1048503	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs10495278	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10495279	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1094602	1.00[EUR][1000 genomes]
rs1094603	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577976	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11580599	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11581037	1.00[CEU][hapmap]
rs11581169	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11582369	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11584418	1.00[CEU][hapmap]
rs11584499	0.90[CHB][hapmap]
rs11586055	1.00[CEU][hapmap]
rs12034268	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12039801	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12088423	1.00[CEU][hapmap]
rs1771486	0.85[EUR][1000 genomes]
rs1803695	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2070960	0.81[ASN][1000 genomes]
rs28587961	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34687764	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3738680	0.90[CHB][hapmap]
rs3738681	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs3795773	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3795774	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3820624	0.81[ASN][1000 genomes]
rs41303083	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4653906	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs4653908	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4653909	0.90[EUR][1000 genomes]
rs4653914	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61825156	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61825157	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61825159	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61827462	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6663726	0.90[EUR][1000 genomes]
rs6668719	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs7530253	1.00[EUR][1000 genomes]
rs7537552	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs9287011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9970544	0.95[AMR][1000 genomes];0.96[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	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
6	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
8	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
9	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription 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 miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10916266	LOC441869	trans	lymphoblastoid	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228298200-228303800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:228298200-228304600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:228298200-228307200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:228298400-228307200	Weak transcription	NHEK	skin
5	chr1:228298800-228307200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:228299800-228307200	Weak transcription	Placenta	Placenta
7	chr1:228300000-228305400	Weak transcription	Fetal Intestine Small	intestine
8	chr1:228301400-228303400	Enhancers	HepG2	liver
9	chr1:228301800-228304400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:228302600-228303200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:228302800-228303400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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