Variant report

Variant	rs4854253
Chromosome Location	chr2:96056112-96056113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:96054686..96057154-chr2:96060298..96063036,4	K562	blood:
2	chr2:96055037..96056846-chr2:96067263..96069030,2	K562	blood:

Variant related genes	Relation type
ENSG00000115042	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10874471	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MKK][hapmap];0.82[YRI][hapmap];0.91[ASN][1000 genomes]
rs11164125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11677429	0.95[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs12373651	0.84[AMR][1000 genomes]
rs12468117	0.89[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes]
rs12468777	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12471472	0.95[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs1345917	0.85[AMR][1000 genomes]
rs1364394	0.95[CEU][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes]
rs2113419	0.90[ASN][1000 genomes]
rs2216793	0.84[AMR][1000 genomes]
rs2320170	0.89[ASW][hapmap];0.95[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs2320431	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3755518	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3772031	0.86[LWK][hapmap];0.82[YRI][hapmap]
rs3772032	0.85[LWK][hapmap];0.82[YRI][hapmap]
rs3772033	0.86[LWK][hapmap];0.82[YRI][hapmap]
rs3866290	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4854251	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs58610630	0.89[ASN][1000 genomes]
rs61649840	0.89[ASN][1000 genomes]
rs67628541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72821422	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72821437	0.85[AMR][1000 genomes]
rs869185	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs870393	0.83[LWK][hapmap];0.82[YRI][hapmap]
rs889852	0.86[LWK][hapmap];0.82[YRI][hapmap]
rs9678800	0.86[LWK][hapmap];0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv1008945	chr2:95745367-96062107	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	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
4	nsv998370	chr2:95897299-96074071	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv535823	chr2:95897299-96074071	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	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
7	nsv528011	chr2:95931218-96057011	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1010831	chr2:95935648-96074213	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv535824	chr2:95935648-96074213	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv998543	chr2:95979772-96074212	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv535825	chr2:95979772-96074212	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv961829	chr2:96043414-96069177	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4854253	ZNF514	cis	parietal	SCAN
rs4854253	MGAT4A	cis	parietal	SCAN
rs4854253	FER1L5	cis	cerebellum	SCAN
rs4854253	AC008268.1	cis	lung	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96051600-96067200	Weak transcription	Right Atrium	heart
2	chr2:96052200-96057400	Weak transcription	Spleen	Spleen
3	chr2:96054600-96056400	Enhancers	Right Ventricle	heart
4	chr2:96054600-96060200	Enhancers	Fetal Intestine Large	intestine
5	chr2:96054800-96060000	Enhancers	Fetal Intestine Small	intestine
6	chr2:96054800-96060000	Enhancers	Pancreas	Pancrea
7	chr2:96054800-96060200	Enhancers	Liver	Liver
8	chr2:96055000-96059600	Enhancers	Duodenum Mucosa	Duodenum
9	chr2:96055400-96056400	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr2:96055400-96057400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:96055400-96067200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:96055400-96067200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:96055400-96067200	Weak transcription	Brain Anterior Caudate	brain
14	chr2:96055600-96056400	Enhancers	Colonic Mucosa	Colon
15	chr2:96055600-96056600	Weak transcription	Ovary	ovary
16	chr2:96055600-96057800	Weak transcription	Adipose Nuclei	Adipose
17	chr2:96055600-96058600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:96055800-96057400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:96055800-96057800	Enhancers	Gastric	stomach
20	chr2:96055800-96058000	Flanking Active TSS	HepG2	liver
21	chr2:96055800-96059400	Enhancers	Fetal Heart	heart
22	chr2:96056000-96056200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr2:96056000-96056400	Enhancers	Placenta	Placenta
24	chr2:96056000-96056600	Enhancers	Left Ventricle	heart
25	chr2:96056000-96056600	Enhancers	Stomach Mucosa	stomach

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