Variant report

Variant	rs12118836
Chromosome Location	chr1:171256038-171256039
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10912698	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10912718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912745	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10912756	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12038209	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12040753	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12044884	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12049309	0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12124080	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12127128	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12954	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16864258	1.00[ASW][hapmap];0.87[LWK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs16864339	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2076320	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421804	1.00[ASW][hapmap];0.82[CEU][hapmap];0.96[GIH][hapmap];0.88[LWK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3766654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72714180	0.87[AFR][1000 genomes]
rs72714189	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs732005	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7877	0.89[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer 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	52 gene(s)	inside rSNPs	diseases
3	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12118836	FMO1	cis	uninvolved skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171249200-171262000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:171252000-171258800	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:171253600-171256400	Enhancers	Fetal Intestine Large	intestine
4	chr1:171253800-171260400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:171255200-171256200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:171255200-171256400	Enhancers	Primary hematopoietic stem cells	blood
7	chr1:171255200-171256400	Enhancers	NHEK	skin
8	chr1:171255200-171256600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:171255200-171261200	Enhancers	Fetal Intestine Small	intestine
10	chr1:171255400-171256400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr1:171255400-171256400	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr1:171255600-171256200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:171255600-171256400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:171255600-171256400	Enhancers	HMEC	breast
15	chr1:171255600-171256400	Enhancers	NHDF-Ad	bronchial
16	chr1:171255800-171256200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:171256000-171257200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr1:171256000-171261800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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