Variant report

Variant	rs409553
Chromosome Location	chr6:145886963-145886964
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 232 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:225)

rs_ID	r²[population]
rs1004752	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1011596	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs1011597	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1045820	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1070516	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1070517	0.89[EUR][1000 genomes]
rs1070519	0.89[EUR][1000 genomes]
rs1070520	0.86[EUR][1000 genomes]
rs10872577	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10872579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11155433	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11155435	0.89[EUR][1000 genomes]
rs11155438	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs11965018	0.84[EUR][1000 genomes]
rs12205752	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12208019	0.90[EUR][1000 genomes]
rs12208812	0.91[EUR][1000 genomes]
rs12211884	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1280275	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1280276	0.92[EUR][1000 genomes]
rs1292333	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1292334	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1292335	0.82[CEU][hapmap]
rs1292336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1292337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1292338	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1292339	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1337839	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1337840	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1337841	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13437042	0.80[EUR][1000 genomes]
rs1415744	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1415746	0.96[CEU][hapmap]
rs1415747	0.96[CEU][hapmap]
rs1509213	0.85[EUR][1000 genomes]
rs1509214	0.84[EUR][1000 genomes]
rs1569540	0.82[EUR][1000 genomes]
rs1883365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs1890171	0.96[CEU][hapmap]
rs1912023	0.88[EUR][1000 genomes]
rs1935612	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1935616	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2064185	1.00[CEU][hapmap]
rs2092263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2092295	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2092296	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2092297	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2096201	0.88[EUR][1000 genomes]
rs2103633	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2142983	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs2179323	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2328704	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs35970782	0.84[AMR][1000 genomes]
rs365747	0.92[EUR][1000 genomes]
rs365869	0.92[EUR][1000 genomes]
rs367065	0.92[EUR][1000 genomes]
rs370112	0.91[EUR][1000 genomes]
rs370654	0.92[EUR][1000 genomes]
rs371186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372904	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs376257	0.91[EUR][1000 genomes]
rs378937	0.97[EUR][1000 genomes]
rs379040	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs383841	0.91[EUR][1000 genomes]
rs385729	0.91[EUR][1000 genomes]
rs387376	0.88[EUR][1000 genomes]
rs392612	0.92[EUR][1000 genomes]
rs397311	0.80[EUR][1000 genomes]
rs398408	0.85[EUR][1000 genomes]
rs400329	0.90[EUR][1000 genomes]
rs401331	0.92[EUR][1000 genomes]
rs401561	0.91[EUR][1000 genomes]
rs405206	0.92[EUR][1000 genomes]
rs407887	0.92[EUR][1000 genomes]
rs408443	0.92[EUR][1000 genomes]
rs411785	0.92[EUR][1000 genomes]
rs412350	0.84[EUR][1000 genomes]
rs414297	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs414600	0.92[EUR][1000 genomes]
rs418701	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs425999	0.88[EUR][1000 genomes]
rs426874	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs427128	0.92[EUR][1000 genomes]
rs4332001	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4335004	0.90[EUR][1000 genomes]
rs434318	0.90[EUR][1000 genomes]
rs435671	0.92[EUR][1000 genomes]
rs436156	0.92[EUR][1000 genomes]
rs436498	0.92[EUR][1000 genomes]
rs437147	0.91[EUR][1000 genomes]
rs439035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs440477	0.91[EUR][1000 genomes]
rs441290	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs443628	0.90[EUR][1000 genomes]
rs4455694	0.83[EUR][1000 genomes]
rs446031	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs446362	0.92[EUR][1000 genomes]
rs448258	0.92[EUR][1000 genomes]
rs450921	0.92[EUR][1000 genomes]
rs451108	0.91[EUR][1000 genomes]
rs451699	0.92[EUR][1000 genomes]
rs453834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4634475	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4896820	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4896821	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4896824	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4896829	0.83[EUR][1000 genomes]
rs4896831	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4896832	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4896833	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4896837	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs4896838	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs4896839	0.83[EUR][1000 genomes]
rs55810423	0.81[EUR][1000 genomes]
rs621382	0.85[EUR][1000 genomes]
rs62438257	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6570692	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6570700	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6570701	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6570703	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6570705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6570706	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6570708	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs6570715	0.81[EUR][1000 genomes]
rs6570719	0.81[EUR][1000 genomes]
rs6899702	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6899900	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6900040	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6901888	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6902404	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6902410	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6903252	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6912079	0.92[EUR][1000 genomes]
rs6913727	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6914203	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6915094	0.92[EUR][1000 genomes]
rs6919684	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6923074	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6925594	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6928007	0.81[EUR][1000 genomes]
rs6930154	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6933161	0.81[EUR][1000 genomes]
rs6941429	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs697053	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs697054	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs697055	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs697056	0.84[EUR][1000 genomes]
rs702304	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs702305	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs702306	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs702307	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs702309	0.87[EUR][1000 genomes]
rs702314	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs702317	0.83[EUR][1000 genomes]
rs702318	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs702319	0.83[EUR][1000 genomes]
rs702320	0.82[EUR][1000 genomes]
rs702321	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs702323	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs702324	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs735535	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs735536	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7746330	0.91[EUR][1000 genomes]
rs7752286	0.96[CEU][hapmap]
rs7753770	0.96[CEU][hapmap]
rs7755253	0.91[EUR][1000 genomes]
rs7755586	0.88[EUR][1000 genomes]
rs7755887	0.90[EUR][1000 genomes]
rs7762536	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7772286	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7772717	0.90[EUR][1000 genomes]
rs7773939	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs857875	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs857877	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs857879	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs857880	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs857881	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs857882	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs857883	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs864148	0.88[EUR][1000 genomes]
rs870491	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9322028	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9322029	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9373463	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9373464	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9373471	0.81[EUR][1000 genomes]
rs9376945	0.92[EUR][1000 genomes]
rs9376950	0.91[EUR][1000 genomes]
rs9376954	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9376955	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9376956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9376957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9376961	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9386128	0.84[EUR][1000 genomes]
rs9390336	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9390338	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9390343	0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap]
rs9390344	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs9390349	0.84[EUR][1000 genomes]
rs9399553	0.92[EUR][1000 genomes]
rs9399555	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399559	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9399561	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs9399564	0.81[EUR][1000 genomes]
rs9399565	0.81[EUR][1000 genomes]
rs9403726	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9403729	0.91[EUR][1000 genomes]
rs9403730	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9403731	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9403734	0.88[EUR][1000 genomes]
rs9403735	0.89[EUR][1000 genomes]
rs9403737	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9403739	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9403741	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9403742	0.92[CEU][hapmap];0.80[JPT][hapmap]
rs9403746	0.81[EUR][1000 genomes]
rs9485018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9485019	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9485021	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs9497357	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9497380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9497395	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9497396	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs952405	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs952406	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1028290	chr6:145819982-145911857	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv886748	chr6:145835917-145911730	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1021041	chr6:145836942-145887333	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1016881	chr6:145840961-145887333	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv538465	chr6:145840961-145887333	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs409553	RP11-545I5.3	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145883000-145889800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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