Variant report

Variant	rs4553396
Chromosome Location	chr11:77282025-77282026
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 212 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:206)

rs_ID	r²[population]
rs11237234	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11237271	0.81[EUR][1000 genomes]
rs11237274	0.81[EUR][1000 genomes]
rs11822592	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11823751	0.81[EUR][1000 genomes]
rs11824150	0.81[EUR][1000 genomes]
rs11825573	0.81[EUR][1000 genomes]
rs11827357	0.80[EUR][1000 genomes]
rs12417215	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12417823	0.81[EUR][1000 genomes]
rs12418152	0.81[EUR][1000 genomes]
rs12418261	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12418559	0.81[EUR][1000 genomes]
rs12418734	0.81[EUR][1000 genomes]
rs12418844	0.81[EUR][1000 genomes]
rs12419186	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12419685	0.81[EUR][1000 genomes]
rs12420021	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12420401	0.80[EUR][1000 genomes]
rs12421391	0.81[EUR][1000 genomes]
rs12421695	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12421699	0.81[EUR][1000 genomes]
rs12574660	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12574999	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12575014	0.81[EUR][1000 genomes]
rs12575150	0.81[EUR][1000 genomes]
rs12575305	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12575763	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12577362	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12577552	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1540179	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1544272	0.81[EUR][1000 genomes]
rs1544273	0.81[EUR][1000 genomes]
rs1544274	0.81[EUR][1000 genomes]
rs17135800	0.81[EUR][1000 genomes]
rs17135807	0.81[EUR][1000 genomes]
rs17135809	0.81[EUR][1000 genomes]
rs17135811	0.81[EUR][1000 genomes]
rs1892869	0.81[EUR][1000 genomes]
rs1893901	0.81[EUR][1000 genomes]
rs1945751	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1986277	0.91[AMR][1000 genomes]
rs1986474	0.81[EUR][1000 genomes]
rs2154973	0.81[EUR][1000 genomes]
rs2154988	0.81[EUR][1000 genomes]
rs2156842	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2186573	0.81[EUR][1000 genomes]
rs2187547	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276415	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276416	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2298820	0.81[EUR][1000 genomes]
rs28421376	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28730304	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28930682	0.81[EUR][1000 genomes]
rs34446294	0.81[EUR][1000 genomes]
rs3781616	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3781617	0.81[EUR][1000 genomes]
rs3819211	0.81[EUR][1000 genomes]
rs3949117	0.81[EUR][1000 genomes]
rs4301811	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4399350	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4486654	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4531493	0.81[EUR][1000 genomes]
rs4606503	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944169	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4944170	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4944171	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4944173	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4944175	0.81[EUR][1000 genomes]
rs4945182	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4945183	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4945186	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4945187	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4945189	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4945190	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4945191	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4945192	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4945197	0.81[EUR][1000 genomes]
rs4945202	0.81[EUR][1000 genomes]
rs4945203	0.81[EUR][1000 genomes]
rs4945204	0.81[EUR][1000 genomes]
rs4945205	0.81[EUR][1000 genomes]
rs4945209	0.81[EUR][1000 genomes]
rs4945210	0.81[EUR][1000 genomes]
rs4945211	0.81[EUR][1000 genomes]
rs4945212	0.81[EUR][1000 genomes]
rs4945213	0.81[EUR][1000 genomes]
rs4945214	0.81[EUR][1000 genomes]
rs4945215	0.81[EUR][1000 genomes]
rs55881536	0.81[EUR][1000 genomes]
rs56175172	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56817084	0.81[EUR][1000 genomes]
rs57332020	0.83[EUR][1000 genomes]
rs57362996	0.81[EUR][1000 genomes]
rs57588070	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57805854	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57935035	0.81[EUR][1000 genomes]
rs58367448	0.81[EUR][1000 genomes]
rs58393579	0.81[EUR][1000 genomes]
rs58395847	0.81[EUR][1000 genomes]
rs58608947	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58720932	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59404463	0.81[EUR][1000 genomes]
rs59459776	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59520338	0.81[EUR][1000 genomes]
rs59581090	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59765258	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59832115	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59969402	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59983642	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60045757	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60132034	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60186049	0.81[EUR][1000 genomes]
rs60842160	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60849458	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60929773	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60948958	0.81[EUR][1000 genomes]
rs61201484	0.81[EUR][1000 genomes]
rs61358482	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61361232	0.81[EUR][1000 genomes]
rs61397357	0.81[EUR][1000 genomes]
rs61468764	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6592736	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6592742	0.81[EUR][1000 genomes]
rs66472445	0.81[EUR][1000 genomes]
rs66488360	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66504136	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66658383	0.81[EUR][1000 genomes]
rs66664368	0.80[EUR][1000 genomes]
rs66675536	0.81[EUR][1000 genomes]
rs66681087	0.81[EUR][1000 genomes]
rs66684353	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66738005	0.81[EUR][1000 genomes]
rs66924979	0.81[EUR][1000 genomes]
rs66991096	0.81[EUR][1000 genomes]
rs67035387	0.81[EUR][1000 genomes]
rs67062156	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67195676	0.81[EUR][1000 genomes]
rs67200285	0.81[EUR][1000 genomes]
rs67230007	0.81[EUR][1000 genomes]
rs67241586	0.81[EUR][1000 genomes]
rs67291795	0.81[EUR][1000 genomes]
rs67313689	0.81[EUR][1000 genomes]
rs67555375	0.81[EUR][1000 genomes]
rs67680371	0.81[EUR][1000 genomes]
rs67724005	0.81[EUR][1000 genomes]
rs67736392	0.81[EUR][1000 genomes]
rs67769372	0.81[EUR][1000 genomes]
rs67775318	0.81[EUR][1000 genomes]
rs67807487	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67843465	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67881763	0.85[EUR][1000 genomes]
rs68013767	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs68052959	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7104540	0.81[EUR][1000 genomes]
rs7105526	0.81[EUR][1000 genomes]
rs7106113	0.81[EUR][1000 genomes]
rs7106659	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7109199	0.81[EUR][1000 genomes]
rs7109398	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7109527	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7109704	0.81[EUR][1000 genomes]
rs7116671	0.81[EUR][1000 genomes]
rs7118516	0.81[EUR][1000 genomes]
rs7119471	0.81[EUR][1000 genomes]
rs7119934	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7120465	0.81[EUR][1000 genomes]
rs7123204	0.81[EUR][1000 genomes]
rs7124030	0.81[EUR][1000 genomes]
rs7124116	0.81[EUR][1000 genomes]
rs7124753	0.81[EUR][1000 genomes]
rs7127803	0.81[EUR][1000 genomes]
rs7128881	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs713083	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7131169	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7131298	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs720383	0.81[EUR][1000 genomes]
rs72931818	0.81[EUR][1000 genomes]
rs72931829	0.81[EUR][1000 genomes]
rs72943487	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72943494	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72943497	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72945524	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72945540	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72945566	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72945586	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72947653	0.81[EUR][1000 genomes]
rs72949614	0.81[EUR][1000 genomes]
rs72949656	0.81[EUR][1000 genomes]
rs73491984	0.81[EUR][1000 genomes]
rs7925252	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7930066	0.81[EUR][1000 genomes]
rs7930885	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7930988	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7931215	0.81[EUR][1000 genomes]
rs7932057	0.81[EUR][1000 genomes]
rs7932111	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7932603	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7933197	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7936904	0.81[EUR][1000 genomes]
rs7939623	0.81[EUR][1000 genomes]
rs7942838	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7947430	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7950612	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7950631	0.81[EUR][1000 genomes]
rs7951172	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv3437433	chr11:77101280-77291686	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv2752651	chr11:77211136-77318279	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4553396	INTS4	Cis_1M	lymphoblastoid	RTeQTL
rs4553396	RP11-91P24.7	cis	Thyroid	GTEx
rs4553396	RP11-91P24.6	cis	Artery Tibial	GTEx
rs4553396	RSF1	Cis_1M	lymphoblastoid	RTeQTL
rs4553396	RP11-91P24.6	cis	Thyroid	GTEx
rs4553396	AAMDC	cis	Artery Tibial	GTEx
rs4553396	RP11-91P24.7	cis	Artery Tibial	GTEx
rs4553396	AAMDC	cis	Thyroid	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77272400-77282600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:77278400-77282600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr11:77278400-77283000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr11:77279200-77283800	Enhancers	Pancreas	Pancrea
5	chr11:77279600-77284800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:77280000-77282800	Enhancers	Fetal Stomach	stomach
7	chr11:77280400-77282400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr11:77280400-77282400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:77280600-77282400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr11:77280600-77282400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:77280600-77282600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr11:77280600-77283000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr11:77280800-77282600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:77280800-77282800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr11:77280800-77299600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:77281000-77283000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr11:77281400-77282600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr11:77281600-77282400	Active TSS	Ovary	ovary
19	chr11:77281800-77282600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:77282000-77282400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr11:77282000-77282400	Enhancers	Fetal Lung	lung

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