Variant report

Variant	rs9999212
Chromosome Location	chr4:120655838-120655839
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10005075	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10005177	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10011345	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10011928	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10014793	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10018153	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10018308	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10019790	1.00[ASN][1000 genomes]
rs10023652	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10023655	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12331776	0.81[EUR][1000 genomes]
rs12502919	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12510467	0.81[EUR][1000 genomes]
rs13112498	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13119146	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13122357	0.81[EUR][1000 genomes]
rs13141413	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13328038	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17005485	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17005677	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2389900	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2389902	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2389904	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2714972	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28535991	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28642385	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28706824	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28723049	0.80[EUR][1000 genomes]
rs28847617	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34209241	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4001169	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4833625	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4834804	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4834805	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4834806	0.93[ASN][1000 genomes]
rs4834808	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs749525	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749526	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs752650	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7669436	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7694773	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7699252	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs874425	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9998665	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS 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
6	esv1802546	chr4:120558608-120675026	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1010638	chr4:120586178-120671835	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1009771	chr4:120590902-120665812	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv1803992	chr4:120649398-120665812	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9999212	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs9999212	RP11-33B1.1	cis	Esophagus Mucosa	GTEx
rs9999212	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120649600-120658200	Enhancers	NHLF	lung
2	chr4:120650200-120658000	Enhancers	HSMMtube	muscle
3	chr4:120650200-120658400	Enhancers	NHDF-Ad	bronchial
4	chr4:120650400-120657200	Weak transcription	Psoas Muscle	Psoas
5	chr4:120651200-120656000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:120651600-120656000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:120651600-120658000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:120651800-120656000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:120651800-120656000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:120652000-120658600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:120652200-120656200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:120652200-120656200	Weak transcription	A549	lung
13	chr4:120652200-120658200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr4:120652800-120656000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:120653000-120656000	Weak transcription	Hela-S3	cervix
16	chr4:120653200-120657200	Weak transcription	Aorta	Aorta
17	chr4:120653400-120656000	Weak transcription	Fetal Stomach	stomach
18	chr4:120653400-120656000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:120653400-120656200	Weak transcription	Fetal Kidney	kidney
20	chr4:120653600-120656000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:120653600-120656000	Weak transcription	Stomach Mucosa	stomach
22	chr4:120654200-120656000	Weak transcription	Fetal Heart	heart
23	chr4:120654400-120658800	Enhancers	Osteobl	bone
24	chr4:120654600-120658200	Enhancers	NH-A	brain
25	chr4:120654800-120658000	Enhancers	HSMM	muscle
26	chr4:120654800-120658800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:120655400-120656000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:120655400-120657400	Enhancers	Fetal Lung	lung
29	chr4:120655600-120657200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:120655800-120656000	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr4:120655800-120656200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr4:120655800-120657000	Enhancers	HMEC	breast
33	chr4:120655800-120657400	Enhancers	Colon Smooth Muscle	Colon
34	chr4:120655800-120658000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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