Variant report

Variant	rs10399841
Chromosome Location	chr1:225213373-225213374
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 174 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:166)

rs_ID	r²[population]
rs10495228	0.81[ASN][1000 genomes]
rs10495229	0.85[ASN][1000 genomes]
rs10495230	0.88[ASN][1000 genomes]
rs12561993	0.89[ASN][1000 genomes]
rs12562085	0.81[ASN][1000 genomes]
rs12562917	0.87[ASN][1000 genomes]
rs12563033	0.89[ASN][1000 genomes]
rs12563286	0.81[ASN][1000 genomes]
rs12563857	0.89[ASN][1000 genomes]
rs12563866	0.87[ASN][1000 genomes]
rs12564683	0.80[ASN][1000 genomes]
rs12564768	0.87[ASN][1000 genomes]
rs12564776	0.87[ASN][1000 genomes]
rs12565019	0.81[ASN][1000 genomes]
rs12565073	0.87[ASN][1000 genomes]
rs12565401	0.84[ASN][1000 genomes]
rs12565439	0.85[ASN][1000 genomes]
rs12565823	0.84[ASN][1000 genomes]
rs12565833	0.87[ASN][1000 genomes]
rs12566396	0.85[ASN][1000 genomes]
rs12566857	0.89[ASN][1000 genomes]
rs12566886	0.85[ASN][1000 genomes]
rs12567069	0.87[ASN][1000 genomes]
rs12567461	0.81[ASN][1000 genomes]
rs12567470	0.81[ASN][1000 genomes]
rs12567499	0.89[ASN][1000 genomes]
rs12567812	0.87[ASN][1000 genomes]
rs12568142	0.89[ASN][1000 genomes]
rs1480104	0.83[ASN][1000 genomes]
rs1482279	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1482280	0.88[ASN][1000 genomes]
rs1506070	0.89[ASN][1000 genomes]
rs1506072	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1542571	0.81[ASN][1000 genomes]
rs1587980	0.89[ASN][1000 genomes]
rs1600532	0.84[ASN][1000 genomes]
rs1600865	0.80[ASN][1000 genomes]
rs16843950	0.84[ASN][1000 genomes]
rs16843956	0.84[ASN][1000 genomes]
rs16843988	0.84[ASN][1000 genomes]
rs16843997	0.84[ASN][1000 genomes]
rs16844005	0.84[ASN][1000 genomes]
rs16844334	0.84[ASN][1000 genomes]
rs16844355	0.84[ASN][1000 genomes]
rs16844377	0.81[ASN][1000 genomes]
rs16844400	0.81[ASN][1000 genomes]
rs16857787	0.81[ASN][1000 genomes]
rs16858145	0.81[ASN][1000 genomes]
rs16858216	0.81[ASN][1000 genomes]
rs16858299	0.80[ASN][1000 genomes]
rs16858661	0.85[ASN][1000 genomes]
rs16858758	0.85[ASN][1000 genomes]
rs16858766	0.85[ASN][1000 genomes]
rs16858829	0.85[ASN][1000 genomes]
rs16858831	0.85[ASN][1000 genomes]
rs16858932	0.85[ASN][1000 genomes]
rs16858962	0.85[ASN][1000 genomes]
rs1905113	0.89[ASN][1000 genomes]
rs1905114	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1905115	0.89[ASN][1000 genomes]
rs1905117	0.89[ASN][1000 genomes]
rs1936629	0.80[ASN][1000 genomes]
rs1982707	0.89[ASN][1000 genomes]
rs2086368	0.84[ASN][1000 genomes]
rs2101143	0.81[ASN][1000 genomes]
rs2128267	0.84[ASN][1000 genomes]
rs2199832	0.80[ASN][1000 genomes]
rs2291227	0.85[ASN][1000 genomes]
rs2406098	0.81[ASN][1000 genomes]
rs2449257	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2449259	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2449260	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2449273	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2449274	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2449276	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2449280	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2449292	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2449311	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2449313	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2449315	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2449316	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2449327	0.88[AMR][1000 genomes]
rs2456335	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2456339	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2456340	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2489300	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2489302	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2489310	0.80[ASN][1000 genomes]
rs2489322	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2489324	0.83[AFR][1000 genomes]
rs2489325	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2489328	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2489330	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2489332	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2489341	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2489344	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2501061	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2501064	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2501066	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2501068	0.83[AMR][1000 genomes]
rs2501072	0.85[AMR][1000 genomes]
rs2501073	0.85[AMR][1000 genomes]
rs2501081	0.81[ASN][1000 genomes]
rs2501120	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2501123	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2501125	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2501127	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2501129	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2501130	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2501134	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2501135	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2501140	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2501141	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2501143	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2501153	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2501156	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3101907	0.84[ASN][1000 genomes]
rs3101908	0.84[ASN][1000 genomes]
rs3101915	0.83[ASN][1000 genomes]
rs3101919	0.84[ASN][1000 genomes]
rs3102114	0.84[ASN][1000 genomes]
rs3105549	0.84[ASN][1000 genomes]
rs3105555	0.84[ASN][1000 genomes]
rs3105570	0.84[ASN][1000 genomes]
rs3105571	0.84[ASN][1000 genomes]
rs3120985	0.84[ASN][1000 genomes]
rs3120992	0.84[ASN][1000 genomes]
rs3128659	0.84[ASN][1000 genomes]
rs3128663	0.84[ASN][1000 genomes]
rs3128665	0.84[ASN][1000 genomes]
rs3128669	0.84[ASN][1000 genomes]
rs3128670	0.84[ASN][1000 genomes]
rs3991317	0.81[ASN][1000 genomes]
rs4342820	0.81[ASN][1000 genomes]
rs4379650	0.81[ASN][1000 genomes]
rs55668169	0.85[ASN][1000 genomes]
rs55681905	0.84[ASN][1000 genomes]
rs55754430	0.81[ASN][1000 genomes]
rs55761817	0.89[ASN][1000 genomes]
rs55785201	0.88[ASN][1000 genomes]
rs55786647	0.89[ASN][1000 genomes]
rs55876129	0.89[ASN][1000 genomes]
rs55962425	0.89[ASN][1000 genomes]
rs56061128	0.84[ASN][1000 genomes]
rs56088704	0.85[ASN][1000 genomes]
rs56152573	0.85[ASN][1000 genomes]
rs56251723	0.88[ASN][1000 genomes]
rs56337810	0.88[ASN][1000 genomes]
rs57889280	0.88[ASN][1000 genomes]
rs60392992	0.84[ASN][1000 genomes]
rs60692803	0.81[ASN][1000 genomes]
rs61466304	0.81[ASN][1000 genomes]
rs6426049	0.81[ASN][1000 genomes]
rs6426052	0.81[ASN][1000 genomes]
rs6662231	0.81[ASN][1000 genomes]
rs6677680	0.81[ASN][1000 genomes]
rs6697156	0.89[ASN][1000 genomes]
rs6702926	0.80[ASN][1000 genomes]
rs729398	0.81[ASN][1000 genomes]
rs7517625	0.84[ASN][1000 genomes]
rs7523949	0.89[ASN][1000 genomes]
rs7531542	0.89[ASN][1000 genomes]
rs7547639	0.83[ASN][1000 genomes]
rs769295	0.82[ASN][1000 genomes]
rs973980	0.81[ASN][1000 genomes]
rs981068	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757773	chr1:225087924-225253274	Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv2759001	chr1:225087924-225253274	Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3438976	chr1:225133567-225248753	Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv873225	chr1:225162060-225373936	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv549262	chr1:225191852-225319898	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv549263	chr1:225202426-225319898	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv1805842	chr1:225208247-225217265	Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv998899	chr1:225210813-225496353	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225204000-225217400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:225205600-225215600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:225205600-225235600	Weak transcription	Pancreas	Pancrea
4	chr1:225211200-225226800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:225213000-225215200	Weak transcription	Primary hematopoietic stem cells	blood

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