Variant report

Variant	rs6425021
Chromosome Location	chr1:186135236-186135237
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10911836	0.90[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11579683	0.95[EUR][1000 genomes]
rs11582026	1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11583483	0.93[EUR][1000 genomes]
rs12120763	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs12123389	0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12124387	1.00[CEU][hapmap]
rs1322376	0.86[CEU][hapmap]
rs16825040	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs2208692	0.83[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2383457	0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56138834	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6673026	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6680616	0.90[EUR][1000 genomes]
rs72707469	0.85[EUR][1000 genomes]
rs7549613	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7552106	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7554865	0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7554872	0.81[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs911743	1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[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	esv3424090	chr1:185679718-186270877	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6425021	FCN1	trans	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186113800-186135800	Weak transcription	Ovary	ovary
2	chr1:186114600-186160800	Weak transcription	Fetal Kidney	kidney
3	chr1:186115400-186135400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:186116400-186135400	Weak transcription	Aorta	Aorta
5	chr1:186116600-186135400	Weak transcription	Lung	lung
6	chr1:186117200-186135800	Weak transcription	Fetal Lung	lung
7	chr1:186122200-186135600	Weak transcription	K562	blood
8	chr1:186133200-186137400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:186133600-186160800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:186133800-186147800	Weak transcription	Left Ventricle	heart
11	chr1:186134000-186137200	Strong transcription	Adipose Nuclei	Adipose
12	chr1:186134600-186136800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:186134600-186139600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:186134600-186152200	Weak transcription	NH-A	brain
15	chr1:186134800-186139800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:186134800-186147000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:186135000-186146400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:186135000-186147800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:186135200-186136200	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:186135200-186137000	Strong transcription	Liver	Liver

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