Variant report

Variant	rs981612
Chromosome Location	chr15:49665062-49665063
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10467992	0.90[JPT][hapmap]
rs10467993	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10851475	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10851476	0.94[ASW][hapmap];0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap]
rs11070685	0.85[YRI][hapmap]
rs11070687	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070692	0.85[JPT][hapmap]
rs11852825	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11854667	0.94[ASW][hapmap];0.83[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12437486	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12591134	0.81[YRI][hapmap]
rs12899761	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12902497	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12903238	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12903904	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12904171	0.93[EUR][1000 genomes]
rs12909779	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12916840	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1429556	0.85[JPT][hapmap]
rs1594188	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1816293	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1864299	0.83[ASW][hapmap];0.83[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1904313	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1904314	0.97[ASN][1000 genomes]
rs1981995	0.83[ASW][hapmap];0.83[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2043036	0.83[CEU][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2099141	0.82[CEU][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163095	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2163096	0.94[ASW][hapmap];0.83[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2247517	0.83[CHB][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2264508	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2413941	0.91[EUR][1000 genomes]
rs2439133	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28374976	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28653543	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28687437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899431	0.83[CEU][hapmap];0.82[CHB][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3098619	0.83[ASW][hapmap];0.83[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.87[LWK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.82[EUR][1000 genomes]
rs3098621	0.83[CEU][hapmap];0.83[CHB][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3105858	0.83[CEU][hapmap];0.83[CHB][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3907313	0.83[CEU][hapmap];0.82[CHB][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4316697	0.80[JPT][hapmap]
rs4393519	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4421927	0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4508377	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4774537	0.83[CEU][hapmap];0.83[CHB][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4775810	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs481466	0.83[ASW][hapmap];0.83[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.87[LWK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs520495	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs609434	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs612803	0.83[CEU][hapmap];0.83[CHB][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs62009779	0.81[EUR][1000 genomes]
rs626295	0.83[ASW][hapmap];0.83[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.87[LWK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs633333	0.81[EUR][1000 genomes]
rs6493356	0.83[CEU][hapmap];0.82[CHB][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs6493357	0.83[CEU][hapmap];0.82[CHB][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6493359	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6493362	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6493363	0.90[JPT][hapmap]
rs6493366	0.88[YRI][hapmap]
rs6493367	0.88[YRI][hapmap]
rs66499252	0.81[EUR][1000 genomes]
rs672777	0.81[EUR][1000 genomes]
rs7162360	0.83[ASW][hapmap];0.83[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7166847	0.83[CEU][hapmap];0.83[CHB][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7168201	0.81[CHB][hapmap];0.93[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7169443	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7173761	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7177959	0.85[YRI][hapmap]
rs7179127	0.83[ASW][hapmap];0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7179237	0.83[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs735495	0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8024102	0.83[ASW][hapmap];0.83[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8025237	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8031480	0.83[ASW][hapmap];0.83[CEU][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.87[LWK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8034112	0.98[AFR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8034747	0.90[JPT][hapmap]
rs8034956	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8035266	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8039512	0.82[CEU][hapmap];0.83[CHB][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8039920	0.81[CEU][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8040116	0.85[YRI][hapmap]
rs8040134	0.83[ASW][hapmap];0.83[CEU][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.84[LWK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8041461	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8182081	0.80[EUR][1000 genomes]
rs919447	0.83[ASW][hapmap];0.83[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9806208	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9806776	0.89[AMR][1000 genomes];0.95[EUR][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	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv442375	chr15:49652524-49684082	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs981612	COPS2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49664400-49665200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:49664400-49665200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:49664400-49665200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr15:49664400-49665600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
5	chr15:49664600-49665200	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr15:49664600-49665200	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr15:49664600-49665200	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr15:49665000-49673200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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