Variant report

Variant	rs425999
Chromosome Location	chr6:145819370-145819371
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 186 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:183)

rs_ID	r²[population]
rs1045820	0.96[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs1070517	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1070519	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1070520	0.87[AMR][1000 genomes]
rs10872577	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10872579	0.96[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs11155433	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11155435	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11155438	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12205752	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12208019	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12208812	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12211884	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1280275	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1280276	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1292333	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1292334	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1292336	0.96[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs1292337	0.96[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs1292339	0.88[CEU][hapmap];0.89[JPT][hapmap]
rs1337839	0.96[CEU][hapmap]
rs1396648	0.82[CEU][hapmap]
rs1509213	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1509214	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1912023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1935612	0.91[EUR][1000 genomes]
rs1935616	0.84[EUR][1000 genomes]
rs2092295	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2092296	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2092297	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2096201	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2103633	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2142978	0.94[JPT][hapmap]
rs2179323	0.83[EUR][1000 genomes]
rs365747	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs365869	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs367065	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs367693	0.82[ASN][1000 genomes]
rs370112	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs370654	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs371186	0.88[EUR][1000 genomes]
rs372904	0.92[EUR][1000 genomes]
rs376257	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs378937	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs379040	0.92[EUR][1000 genomes]
rs383841	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs385729	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs387376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392612	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs397311	0.80[EUR][1000 genomes]
rs398408	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs399516	0.86[EUR][1000 genomes]
rs400329	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs401331	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs401561	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs405206	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs407887	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs408443	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs409553	0.88[EUR][1000 genomes]
rs411785	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs412350	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs414297	0.92[EUR][1000 genomes]
rs414600	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs418701	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs426874	0.87[EUR][1000 genomes]
rs427128	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4332001	0.85[EUR][1000 genomes]
rs4335004	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs434318	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs435671	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs436156	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs436498	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs437147	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs439035	0.88[EUR][1000 genomes]
rs440477	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs441290	0.88[EUR][1000 genomes]
rs443628	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4455694	0.84[AMR][1000 genomes]
rs446031	0.88[EUR][1000 genomes]
rs446362	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs448258	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs450921	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs451108	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs451699	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs453834	0.88[EUR][1000 genomes]
rs4634475	0.82[EUR][1000 genomes]
rs4896820	0.88[EUR][1000 genomes]
rs4896821	0.87[EUR][1000 genomes]
rs4896824	0.86[EUR][1000 genomes]
rs4896829	0.83[ASN][1000 genomes]
rs4896831	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs4896832	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4896833	0.96[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs4896837	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes]
rs4896838	0.92[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes]
rs4896839	0.84[AMR][1000 genomes]
rs621382	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6570692	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6570700	0.86[EUR][1000 genomes]
rs6570701	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6570703	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes]
rs6570705	0.96[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs6570706	0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs6570708	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6899702	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6899900	0.88[EUR][1000 genomes]
rs6900040	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6901888	0.84[AMR][1000 genomes]
rs6902404	0.87[EUR][1000 genomes]
rs6902410	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6912079	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6913727	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6914203	0.91[EUR][1000 genomes]
rs6915094	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6919684	0.88[EUR][1000 genomes]
rs6923074	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6925594	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6932863	0.82[AMR][1000 genomes]
rs6941429	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs697053	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs697054	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes]
rs697055	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes]
rs697056	0.84[AMR][1000 genomes]
rs702304	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs702305	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs702306	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs702307	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs702309	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs702316	0.94[JPT][hapmap]
rs702317	0.84[AMR][1000 genomes]
rs702318	0.92[CEU][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes]
rs702319	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes]
rs702320	0.84[AMR][1000 genomes]
rs702322	0.94[JPT][hapmap]
rs702324	0.92[CEU][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes]
rs7746330	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7755253	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7755586	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7755887	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7762536	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7772717	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7773939	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs857875	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs857877	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs857879	0.96[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs857880	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs857881	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs857882	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs857883	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs864148	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs870491	0.86[EUR][1000 genomes]
rs9322028	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9322029	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9373463	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9373464	0.91[EUR][1000 genomes]
rs9373467	0.89[JPT][hapmap]
rs9376945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9376950	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9376954	0.84[EUR][1000 genomes]
rs9376955	0.89[CEU][hapmap];0.80[JPT][hapmap]
rs9376956	0.96[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs9376957	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs9390336	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9390338	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9390343	0.92[CEU][hapmap]
rs9390344	0.88[CEU][hapmap];0.84[JPT][hapmap]
rs9399553	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9399555	0.88[EUR][1000 genomes]
rs9399559	0.83[EUR][1000 genomes]
rs9399561	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9403726	0.91[EUR][1000 genomes]
rs9403729	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9403730	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9403731	0.91[EUR][1000 genomes]
rs9403734	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9403735	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9403737	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9403739	0.96[CEU][hapmap];0.94[JPT][hapmap]
rs9497357	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9497380	0.96[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs9497395	0.96[CEU][hapmap];0.83[JPT][hapmap]
rs952405	0.86[EUR][1000 genomes]
rs952406	0.84[EUR][1000 genomes];0.87[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	nsv604838	chr6:145709371-145841146	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv886746	chr6:145815949-145920894	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv886747	chr6:145815949-145922777	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs425999	RP11-545I5.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145819000-145819600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:145819000-145820600	Enhancers	Stomach Mucosa	stomach

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