Variant report

Variant	rs12923231
Chromosome Location	chr16:69572892-69572893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:69563250..69565350-chr16:69571620..69573342,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11640319	0.83[ASW][hapmap];0.88[MKK][hapmap];0.84[YRI][hapmap]
rs11646575	0.91[AFR][1000 genomes]
rs12599391	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12924872	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12929503	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12933292	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13330951	0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[ASN][1000 genomes]
rs1364063	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1437134	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap]
rs1469908	0.88[MKK][hapmap];0.84[YRI][hapmap]
rs1972659	0.87[AFR][1000 genomes]
rs2032912	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2161630	0.83[ASW][hapmap];0.90[MKK][hapmap];0.84[YRI][hapmap]
rs244415	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs244417	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap]
rs244418	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes]
rs244420	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs2917670	0.85[MKK][hapmap];0.84[YRI][hapmap]
rs35967356	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3848278	0.83[ASW][hapmap];0.91[MKK][hapmap];0.84[YRI][hapmap]
rs4783721	0.96[CEU][hapmap];0.89[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4783722	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56096139	0.95[ASN][1000 genomes]
rs62052815	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62052816	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6499240	0.96[CEU][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap]
rs6499244	0.92[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap]
rs669696	0.85[EUR][1000 genomes]
rs7187634	0.83[ASW][hapmap];0.88[MKK][hapmap];0.84[YRI][hapmap]
rs7191292	0.83[ASW][hapmap];0.86[MKK][hapmap];0.84[YRI][hapmap]
rs7192380	0.83[ASW][hapmap];0.88[MKK][hapmap];0.84[YRI][hapmap]
rs7359336	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap]
rs8049728	0.83[ASW][hapmap];0.88[MKK][hapmap];0.84[YRI][hapmap]
rs8055756	0.81[ASW][hapmap];0.88[MKK][hapmap];0.84[YRI][hapmap]
rs8061052	0.84[YRI][hapmap]
rs862320	0.81[EUR][1000 genomes]
rs889398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs889399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431514	chr16:69428599-69581699	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats 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 target site	31 gene(s)	inside rSNPs	diseases
2	nsv906821	chr16:69509506-69576894	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1852	chr16:69566121-69610962	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12923231	FBXL8	cis	parietal	SCAN
rs12923231	MTSS1L	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69569800-69573000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr16:69569800-69573000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr16:69569800-69573200	Weak transcription	A549	lung
4	chr16:69569800-69573200	Weak transcription	HSMM	muscle
5	chr16:69569800-69576800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr16:69569800-69576800	Weak transcription	NHLF	lung
7	chr16:69569800-69579800	Weak transcription	Placenta	Placenta
8	chr16:69570000-69573000	Weak transcription	HMEC	breast
9	chr16:69570000-69573400	Weak transcription	NHEK	skin
10	chr16:69570000-69577000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr16:69570800-69574000	Enhancers	NHDF-Ad	bronchial
12	chr16:69571400-69575400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr16:69571600-69573000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr16:69571600-69573000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr16:69571600-69573800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr16:69571800-69573000	Weak transcription	HSMMtube	muscle
17	chr16:69571800-69574000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr16:69571800-69574000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr16:69572400-69573000	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr16:69572600-69574000	Enhancers	Osteobl	bone
21	chr16:69572600-69574600	Enhancers	Hela-S3	cervix
22	chr16:69572600-69575800	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr16:69572800-69573400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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