Variant report

Variant	rs232905
Chromosome Location	chr1:59104500-59104501
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	chr1:59104270..59106295-chr1:59109076..59111126,2	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs11207300	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11576450	0.86[ASN][1000 genomes]
rs11578449	0.86[ASN][1000 genomes]
rs11578722	0.86[ASN][1000 genomes]
rs11578726	0.86[ASN][1000 genomes]
rs11579447	0.91[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs11580213	0.86[ASN][1000 genomes]
rs11581243	0.86[ASN][1000 genomes]
rs11582157	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11584050	0.86[ASN][1000 genomes]
rs11588089	0.92[ASN][1000 genomes]
rs11811899	0.86[ASN][1000 genomes]
rs12562546	0.86[ASN][1000 genomes]
rs12564701	0.86[ASN][1000 genomes]
rs13374003	0.86[ASN][1000 genomes]
rs13375494	0.83[ASN][1000 genomes]
rs13375496	0.81[ASN][1000 genomes]
rs1492719	0.86[ASN][1000 genomes]
rs15307	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs170828	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17264915	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2064373	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2206764	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2273045	0.86[ASN][1000 genomes]
rs232778	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232784	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[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs232788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232790	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[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232878	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs232879	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs232880	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232886	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232901	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232902	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232904	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232906	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232907	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232908	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232909	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs232910	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs232911	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2746077	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2746083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34204484	0.86[ASN][1000 genomes]
rs35584156	0.86[ASN][1000 genomes]
rs36084158	0.86[ASN][1000 genomes]
rs4912369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912372	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs513436	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[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542750	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[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55742964	0.86[ASN][1000 genomes]
rs56097207	0.86[ASN][1000 genomes]
rs57166198	0.86[ASN][1000 genomes]
rs58488453	0.86[ASN][1000 genomes]
rs58575274	0.86[ASN][1000 genomes]
rs58626572	0.86[ASN][1000 genomes]
rs59450768	0.86[ASN][1000 genomes]
rs59469255	0.86[ASN][1000 genomes]
rs59590779	0.86[ASN][1000 genomes]
rs60217618	0.86[ASN][1000 genomes]
rs60382465	0.86[ASN][1000 genomes]
rs60698357	0.86[ASN][1000 genomes]
rs60869327	0.86[ASN][1000 genomes]
rs61070091	0.86[ASN][1000 genomes]
rs61203902	0.86[ASN][1000 genomes]
rs61552468	0.86[ASN][1000 genomes]
rs6661394	0.86[ASN][1000 genomes]
rs6661513	0.86[ASN][1000 genomes]
rs6661551	0.86[ASN][1000 genomes]
rs6661592	0.86[ASN][1000 genomes]
rs6661922	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661969	0.86[ASN][1000 genomes]
rs6686203	0.86[ASN][1000 genomes]
rs675871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688225	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72676714	0.86[ASN][1000 genomes]
rs72676715	0.86[ASN][1000 genomes]
rs72676717	0.86[ASN][1000 genomes]
rs72676720	0.86[ASN][1000 genomes]
rs72676723	0.86[ASN][1000 genomes]
rs72676724	0.86[ASN][1000 genomes]
rs72676726	0.86[ASN][1000 genomes]
rs72676729	0.86[ASN][1000 genomes]
rs72676731	0.86[ASN][1000 genomes]
rs72678808	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72678814	0.82[EUR][1000 genomes];0.92[ASN][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	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs232905	C1orf177	cis	parietal	SCAN
rs232905	TACSTD2	cis	multi-tissue	Pritchard
rs232905	DAB1	cis	cerebellum	SCAN
rs232905	MYSM1	cis	cerebellum	SCAN
rs232905	OMA1	cis	parietal	SCAN
rs232905	OMA1	cis	cerebellum	SCAN
rs232905	MYSM1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59093200-59115400	Weak transcription	NHEK	skin
2	chr1:59096000-59121600	Weak transcription	HUVEC	blood vessel
3	chr1:59096600-59121600	Weak transcription	Gastric	stomach
4	chr1:59101600-59109400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:59102000-59130400	Weak transcription	Aorta	Aorta
6	chr1:59103600-59115200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:59104000-59104600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:59104000-59104600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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