Variant report

Variant	rs3866290
Chromosome Location	chr2:96081230-96081231
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:96081200-96081950	K562	blood:	n/a	n/a
2	POLR2A	chr2:96081069-96081659	K562	blood:	n/a	n/a
3	POLR2A	chr2:96081225-96082271	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:96075502..96078062-chr2:96080565..96082450,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNIP3-4	chr2:96080756-96082345	NONHSAT072486

Variant related genes	Relation type
ENSG00000248821	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11164125	0.89[AMR][1000 genomes]
rs12373651	0.84[AMR][1000 genomes]
rs12468117	0.81[AMR][1000 genomes]
rs12471472	0.81[AMR][1000 genomes]
rs1345917	0.81[AMR][1000 genomes]
rs1364394	0.81[AMR][1000 genomes]
rs4854253	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67628541	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72821422	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72821437	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv817299	chr2:95799814-96159275	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv998014	chr2:95913278-96296630	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv2757818	chr2:95970138-96152559	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	esv2759076	chr2:95970138-96152559	Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv961449	chr2:96069177-96081253	Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3416818	chr2:96072529-96680708	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3866290	AC008268.1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96070000-96082000	Weak transcription	Brain Anterior Caudate	brain
2	chr2:96070000-96083000	Weak transcription	Right Atrium	heart
3	chr2:96070200-96081400	Weak transcription	Pancreas	Pancrea
4	chr2:96074400-96081800	Weak transcription	A549	lung
5	chr2:96074600-96082600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:96077200-96081400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:96077600-96084800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:96079000-96082200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:96079600-96081400	Weak transcription	Brain Germinal Matrix	brain
10	chr2:96079600-96081600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:96079600-96081600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:96079600-96082200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:96079600-96084000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:96079800-96081400	Weak transcription	Fetal Lung	lung
15	chr2:96079800-96081600	Weak transcription	Fetal Brain Female	brain
16	chr2:96079800-96081800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:96079800-96082000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:96079800-96082000	Weak transcription	Fetal Muscle Leg	muscle
19	chr2:96079800-96083000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:96080000-96081800	Weak transcription	Fetal Intestine Large	intestine
21	chr2:96080200-96082800	Weak transcription	Fetal Stomach	stomach
22	chr2:96080600-96082200	Weak transcription	Fetal Intestine Small	intestine

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