Variant report

Variant	rs1274409
Chromosome Location	chr10:92362797-92362798
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1274394	0.94[ASN][1000 genomes]
rs1274398	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1274404	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1274405	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1274406	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274407	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274408	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274410	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1290000	0.80[ASN][1000 genomes]
rs1299939	0.99[ASN][1000 genomes]
rs1419342	0.84[ASN][1000 genomes]
rs1419343	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547852	0.93[AFR][1000 genomes]
rs1573251	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1779941	0.99[ASN][1000 genomes]
rs1857593	0.86[ASN][1000 genomes]
rs1857594	0.86[ASN][1000 genomes]
rs1936574	0.85[ASN][1000 genomes]
rs1936575	0.81[ASN][1000 genomes]
rs1936577	0.84[ASN][1000 genomes]
rs1936578	0.86[ASN][1000 genomes]
rs1936579	0.86[ASN][1000 genomes]
rs1936580	0.86[ASN][1000 genomes]
rs1936583	0.90[ASN][1000 genomes]
rs1936584	0.88[ASN][1000 genomes]
rs1936585	0.88[ASN][1000 genomes]
rs1936586	0.88[ASN][1000 genomes]
rs1936587	0.88[ASN][1000 genomes]
rs1936599	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1936617	0.84[ASN][1000 genomes]
rs1954506	0.90[ASN][1000 genomes]
rs2051154	0.92[ASN][1000 genomes]
rs2051155	0.92[ASN][1000 genomes]
rs2096348	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2211559	0.86[ASN][1000 genomes]
rs2226213	0.84[ASN][1000 genomes]
rs2253139	0.83[ASN][1000 genomes]
rs2253576	0.84[ASN][1000 genomes]
rs2253577	0.84[ASN][1000 genomes]
rs2255628	0.99[ASN][1000 genomes]
rs2263616	0.81[ASN][1000 genomes]
rs2263617	0.84[ASN][1000 genomes]
rs2263618	0.84[ASN][1000 genomes]
rs2263619	0.84[ASN][1000 genomes]
rs2263620	0.84[ASN][1000 genomes]
rs2420189	0.86[ASN][1000 genomes]
rs2420190	0.86[ASN][1000 genomes]
rs2420191	0.86[ASN][1000 genomes]
rs2420192	0.86[ASN][1000 genomes]
rs2465117	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2465118	0.86[ASN][1000 genomes]
rs2489293	0.86[ASN][1000 genomes]
rs2489294	0.84[ASN][1000 genomes]
rs2490322	0.80[ASN][1000 genomes]
rs2710717	0.97[ASN][1000 genomes]
rs2710725	0.85[ASN][1000 genomes]
rs2710726	0.89[ASN][1000 genomes]
rs2710728	0.99[ASN][1000 genomes]
rs2710733	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2710734	0.88[ASN][1000 genomes]
rs2710735	0.86[ASN][1000 genomes]
rs2710736	0.86[ASN][1000 genomes]
rs2710737	0.86[ASN][1000 genomes]
rs2710738	0.86[ASN][1000 genomes]
rs2710739	0.86[ASN][1000 genomes]
rs2710744	0.86[ASN][1000 genomes]
rs2710751	0.81[ASN][1000 genomes]
rs2710755	0.84[ASN][1000 genomes]
rs2710756	0.84[ASN][1000 genomes]
rs2710759	0.84[ASN][1000 genomes]
rs2800119	0.91[AFR][1000 genomes]
rs2800128	0.92[ASN][1000 genomes]
rs2800131	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800163	0.84[ASN][1000 genomes]
rs2800164	0.84[ASN][1000 genomes]
rs2800165	0.84[ASN][1000 genomes]
rs2800166	0.83[ASN][1000 genomes]
rs2800167	0.83[ASN][1000 genomes]
rs2800170	0.84[ASN][1000 genomes]
rs2800174	0.84[ASN][1000 genomes]
rs2800176	0.81[ASN][1000 genomes]
rs2800177	0.86[ASN][1000 genomes]
rs2800179	0.86[ASN][1000 genomes]
rs2800180	0.86[ASN][1000 genomes]
rs2800182	0.86[ASN][1000 genomes]
rs2800183	0.86[ASN][1000 genomes]
rs2800188	0.88[ASN][1000 genomes]
rs2800189	0.86[ASN][1000 genomes]
rs2800190	0.86[ASN][1000 genomes]
rs2800191	0.85[ASN][1000 genomes]
rs2800192	0.86[ASN][1000 genomes]
rs2800193	0.86[ASN][1000 genomes]
rs2800194	0.88[ASN][1000 genomes]
rs2800195	0.86[ASN][1000 genomes]
rs7475208	0.83[ASN][1000 genomes]
rs7478197	0.82[ASN][1000 genomes]
rs7903113	0.85[ASN][1000 genomes]
rs9731151	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422237	chr10:91940542-92547558	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1052753	chr10:92081093-92565617	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv467432	chr10:92082250-92559908	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv551879	chr10:92082250-92559908	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv467433	chr10:92083015-92598458	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv551880	chr10:92083015-92598458	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv516743	chr10:92083015-92605119	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1036256	chr10:92083932-92459915	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1049931	chr10:92083932-92605364	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv948363	chr10:92084520-92614402	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv551881	chr10:92090785-92457733	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv551882	chr10:92090785-92598823	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1047255	chr10:92095431-92548184	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv540744	chr10:92095431-92548184	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv1054504	chr10:92099335-92590723	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1274409	IFIT3	cis	cerebellum	SCAN
rs1274409	PDE6C	cis	cerebellum	SCAN
rs1274409	PAPSS2	cis	parietal	SCAN
rs1274409	LDB3	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:92361600-92362800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr10:92362200-92363200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr10:92362400-92363000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr10:92362400-92363200	Enhancers	Osteobl	bone
5	chr10:92362400-92363400	Enhancers	HMEC	breast
6	chr10:92362400-92363600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr10:92362400-92364600	Enhancers	HSMM	muscle
8	chr10:92362400-92364600	Enhancers	HSMMtube	muscle
9	chr10:92362400-92365200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr10:92362600-92362800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr10:92362600-92363200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr10:92362600-92364000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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