Variant report

Variant	rs2893226
Chromosome Location	chr1:93288437-93288438
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	chr1:93286088..93289627-chr1:93296091..93300055,5	K562	blood:
2	chr1:93287112..93289534-chr1:93296366..93298267,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122406	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10874745	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164803	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164814	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164820	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs11164825	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11164857	1.00[CHB][hapmap]
rs11577426	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11578004	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11578098	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11582791	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586089	1.00[ASN][1000 genomes]
rs11586570	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800409	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11800771	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11800848	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs11803097	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11810217	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12062315	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12081675	1.00[JPT][hapmap]
rs12082659	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12726286	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728322	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12731107	1.00[JPT][hapmap]
rs12738964	0.84[AMR][1000 genomes]
rs12743005	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12746893	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs12746956	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747275	1.00[JPT][hapmap]
rs12749786	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs12750269	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1415296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs17381426	1.00[CHB][hapmap]
rs17614449	0.84[AMR][1000 genomes]
rs1854797	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34041593	0.86[ASN][1000 genomes]
rs34098754	0.86[ASN][1000 genomes]
rs34168045	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34202284	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34244251	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35031391	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35051335	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35183060	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790450	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4642892	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs58270016	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604026	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66525381	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657809	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66649041	0.84[AMR][1000 genomes]
rs6687931	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71652510	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514280	0.91[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521417	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554594	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv530047	chr1:93273425-93308213	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2893226	FAM69A	cis	parietal	SCAN
rs2893226	FAM69A	cis	cerebellum	SCAN
rs2893226	FAM69A	cis	Artery Tibial	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93284000-93288600	Weak transcription	Stomach Mucosa	stomach
2	chr1:93286200-93288600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:93286200-93288600	Weak transcription	HMEC	breast
4	chr1:93286400-93288600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:93286400-93288600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:93286400-93288600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:93286400-93288600	Weak transcription	Osteobl	bone
8	chr1:93286400-93288800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:93286600-93288600	Weak transcription	NHEK	skin
10	chr1:93287600-93289000	Enhancers	Placenta	Placenta
11	chr1:93287800-93289200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:93288000-93288800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:93288000-93289800	Enhancers	HepG2	liver
14	chr1:93288400-93288600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:93288400-93289600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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