Variant report

Variant	rs1119266
Chromosome Location	chr1:153097240-153097241
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10888533	0.83[EUR][1000 genomes]
rs11205209	0.95[EUR][1000 genomes]
rs11577955	0.88[ASN][1000 genomes]
rs11578865	0.91[CHB][hapmap]
rs11585767	0.91[CHB][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap]
rs11586440	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12734959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12752746	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1392806	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1500941	0.87[ASW][hapmap];0.96[CEU][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs1604264	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2928	0.95[EUR][1000 genomes]
rs310133	1.00[ASN][1000 genomes]
rs34115170	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34863954	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35225843	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs547119	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs61811924	0.95[EUR][1000 genomes]
rs6679004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
6	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
7	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv464017	chr1:153033406-153099345	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv547920	chr1:153033406-153099345	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv1004168	chr1:153088209-153226033	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1119266	LCE1C	cis	parietal	SCAN
rs1119266	LCE3B	cis	cerebellum	SCAN
rs1119266	RAB13	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153095200-153097400	Enhancers	H1 Cell Line	embryonic stem cell
2	chr1:153095600-153098000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:153095600-153099000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
4	chr1:153095800-153100000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:153096000-153099400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:153096200-153099400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:153096200-153099400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:153096400-153099400	Weak transcription	NHEK	skin
9	chr1:153096800-153098600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
10	chr1:153097000-153097400	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:153097000-153097400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:153097000-153097400	Enhancers	H9 Cell Line	embryonic stem cell
13	chr1:153097000-153097400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:153097000-153097400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:153097000-153097800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
16	chr1:153097000-153098000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
17	chr1:153097200-153097400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr1:153097200-153097400	ZNF genes & repeats	Pancreas	Pancrea

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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