Variant report

Variant	rs10121899
Chromosome Location	chr9:21770951-21770952
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10114559	0.91[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10119568	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10119693	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10121449	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10738598	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10738601	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10757244	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10757257	0.89[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10811597	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10811598	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10811603	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10811608	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10811623	0.84[EUR][1000 genomes]
rs10811625	0.87[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10811626	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10811629	0.91[CHB][hapmap];0.80[CHD][hapmap];0.82[TSI][hapmap]
rs10965117	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10965128	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10965133	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10965134	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10965135	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10965141	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10965143	0.83[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10965144	0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10965145	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10965153	0.91[CHB][hapmap]
rs12555601	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13298275	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1335503	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1335510	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1335511	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1341866	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1345020	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1345023	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1345024	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1414243	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1414253	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1561650	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2165409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3900787	0.88[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3922992	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4265275	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4364717	0.85[CEU][hapmap]
rs4615669	0.90[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7022754	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7023329	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs7023954	0.88[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7029036	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7033879	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038523	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7049092	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7863090	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7863942	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs958219	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892743	chr9:21675545-21772064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1026981	chr9:21748202-21811697	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	nsv1016579	chr9:21756285-21785335	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10121899	MLLT3	cis	cerebellum	SCAN
rs10121899	MTAP	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21765400-21772600	Weak transcription	HSMM	muscle
2	chr9:21767200-21771000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:21770200-21772000	Enhancers	HMEC	breast
4	chr9:21770400-21771000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:21770400-21772000	Enhancers	Hela-S3	cervix
6	chr9:21770400-21772800	Enhancers	NHLF	lung
7	chr9:21770400-21773400	Enhancers	Stomach Mucosa	stomach
8	chr9:21770600-21771000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:21770600-21771000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:21770600-21771000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr9:21770600-21771000	Enhancers	NHDF-Ad	bronchial
12	chr9:21770600-21771000	Enhancers	NHEK	skin
13	chr9:21770600-21771000	Enhancers	Osteobl	bone
14	chr9:21770600-21771400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:21770600-21771800	Enhancers	NH-A	brain
16	chr9:21770600-21772000	Enhancers	HUVEC	blood vessel
17	chr9:21770600-21775800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr9:21770800-21771000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:21770800-21771400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:21770800-21771800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:21770800-21771800	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr9:21770800-21773000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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