Variant report

Variant	rs2816168
Chromosome Location	chr1:179204075-179204076
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179198432..179201318-chr1:179202068..179205329,4	K562	blood:
2	chr1:179198308..179201029-chr1:179203787..179207295,3	MCF-7	breast:
3	chr1:179198578..179200857-chr1:179201738..179204176,2	K562	blood:

Variant related genes	Relation type
ENSG00000143322	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1078872	0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs10913690	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs10913692	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[TSI][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs10913693	0.82[EUR][1000 genomes]
rs10913697	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs12130276	0.86[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap]
rs12132572	0.84[ASN][1000 genomes]
rs1325195	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1763022	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1807916	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1826183	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1856968	0.82[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs2050923	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2066279	0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2130576	0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2171958	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2171959	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs2306941	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2486998	0.85[EUR][1000 genomes]
rs2487563	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2493123	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2493124	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs2636265	0.91[ASN][1000 genomes]
rs2636272	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2636274	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs2636276	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs2636277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2636278	0.80[GIH][hapmap]
rs2636280	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2636282	0.91[ASN][1000 genomes]
rs2636291	0.84[EUR][1000 genomes]
rs2636293	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap]
rs2791936	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2791940	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2791941	0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs2791944	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2791945	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2793790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2793794	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2793796	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs2793797	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs2793798	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2793800	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2793801	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2793802	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793803	0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2793810	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793812	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2793813	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2793816	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs2816166	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.86[EUR][1000 genomes]
rs2816183	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2816184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2816186	0.95[CHB][hapmap]
rs2816187	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2816190	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs2816191	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2816193	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs2816197	0.87[ASN][1000 genomes]
rs2816198	0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2816199	0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2816200	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2816201	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2816202	0.87[ASN][1000 genomes]
rs2816203	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2816204	0.86[ASN][1000 genomes]
rs2816207	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2816208	0.91[ASN][1000 genomes]
rs2816211	0.91[ASN][1000 genomes]
rs2816212	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2816213	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs2816214	0.91[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2816218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3121198	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3122376	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs377785	0.90[ASN][1000 genomes]
rs3813642	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs3813643	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs3829794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes]
rs411266	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs413613	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs434283	0.90[ASN][1000 genomes]
rs451088	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs4651013	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs915337	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs9286921	0.84[EUR][1000 genomes]
rs9425839	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9662858	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs9726961	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs9728480	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs9729129	0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2816168	FAM20B	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179199400-179210000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:179199800-179204600	Enhancers	Hela-S3	cervix
3	chr1:179201200-179204400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:179201200-179204400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:179201200-179204600	Enhancers	HMEC	breast
6	chr1:179201200-179204600	Enhancers	NHEK	skin
7	chr1:179202600-179204400	Enhancers	HUVEC	blood vessel
8	chr1:179203000-179204400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:179203000-179204400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr1:179203000-179204600	Enhancers	NHDF-Ad	bronchial
11	chr1:179203400-179204600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:179203600-179204400	Enhancers	K562	blood
13	chr1:179203600-179204600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:179203600-179204600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:179203800-179204400	Enhancers	A549	lung
16	chr1:179203800-179212400	Weak transcription	HepG2	liver
17	chr1:179204000-179204200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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