Variant report

Variant	rs1558701
Chromosome Location	chr2:37027819-37027820
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:37026211..37031295-chr2:37031745..37037130,6	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1014584	0.81[CEU][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs10179017	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10180537	0.88[CHB][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10198181	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10200548	0.81[CEU][hapmap]
rs10209211	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11124543	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11124545	0.81[EUR][1000 genomes]
rs11124546	0.85[CHB][hapmap];0.91[ASN][1000 genomes]
rs11692052	0.80[AMR][1000 genomes]
rs11902881	0.92[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs12618630	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12618670	0.93[ASN][1000 genomes]
rs12622304	0.90[ASN][1000 genomes]
rs17019851	0.92[CHB][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs17019854	0.92[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs2041809	0.85[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap]
rs2058683	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2072527	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2276668	0.83[ASN][1000 genomes]
rs2276669	0.81[ASN][1000 genomes]
rs2372713	0.90[CEU][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34040386	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3821147	0.89[JPT][hapmap]
rs4670169	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs4670171	0.90[CEU][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4670615	0.89[ASN][1000 genomes]
rs4670616	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4670618	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57032858	0.89[ASN][1000 genomes]
rs6544039	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6544040	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6544041	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6544042	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6721362	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72867896	0.99[ASN][1000 genomes]
rs7606098	0.86[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763724	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879613	0.89[JPT][hapmap]
rs879614	0.89[JPT][hapmap]
rs929640	0.92[CHB][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][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	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv428395	chr2:36990348-37300352	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv2682	chr2:37015550-37060432	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1011014	chr2:37027819-37095895	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1558701	MORN2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37013000-37033000	Weak transcription	Ovary	ovary
2	chr2:37024400-37028400	Enhancers	Primary T cells fromperipheralblood	blood
3	chr2:37024400-37033800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:37025200-37033000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:37027400-37044200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:37027600-37028200	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr2:37027600-37036200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:37027800-37028000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr2:37027800-37028200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr2:37027800-37028200	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr2:37027800-37028400	Enhancers	GM12878-XiMat	blood

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