Variant report

Variant	rs11164125
Chromosome Location	chr2:96057129-96057130
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	chr2:96056371..96059233-chr2:96066001..96068582,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115042	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10874471	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11164122	1.00[YRI][hapmap]
rs11677429	0.95[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes]
rs11897976	1.00[ASW][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap]
rs12373651	0.83[AMR][1000 genomes]
rs12468117	0.89[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes]
rs12468777	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12471472	0.95[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes]
rs1345917	0.87[AMR][1000 genomes]
rs1364394	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes]
rs1862897	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs2042477	1.00[YRI][hapmap]
rs2113417	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[YRI][hapmap]
rs2113419	0.89[ASN][1000 genomes]
rs2216793	0.86[AMR][1000 genomes]
rs2320170	0.95[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs2320431	1.00[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs3755518	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs3755520	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[YRI][hapmap]
rs3755521	1.00[YRI][hapmap]
rs3755523	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs3772041	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs3772042	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs3772043	1.00[YRI][hapmap]
rs3821341	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs3866290	0.89[AMR][1000 genomes]
rs4854251	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4854253	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]
rs58610630	0.90[ASN][1000 genomes]
rs61649840	0.90[ASN][1000 genomes]
rs6577012	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6715813	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6741001	1.00[YRI][hapmap]
rs6750542	0.82[YRI][hapmap]
rs67628541	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72821422	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72821437	0.87[AMR][1000 genomes]
rs7574862	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs7580685	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs7594144	1.00[YRI][hapmap]
rs869185	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs889851	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap]
rs889853	1.00[YRI][hapmap]
rs918811	1.00[ASW][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap]
rs9989786	1.00[ASW][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
8	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
9	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
10	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
11	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
12	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
13	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11164125	ADRA2B	cis	Thyroid	GTEx
rs11164125	ZNF514	cis	parietal	SCAN
rs11164125	FER1L5	cis	cerebellum	SCAN
rs11164125	AC008268.1	cis	lung	GTEx
rs11164125	MGAT4A	cis	parietal	SCAN

Chromatin state (count:24 , 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	chr2:96054600-96060200	Enhancers	Fetal Intestine Large	intestine
4	chr2:96054800-96060000	Enhancers	Fetal Intestine Small	intestine
5	chr2:96054800-96060000	Enhancers	Pancreas	Pancrea
6	chr2:96054800-96060200	Enhancers	Liver	Liver
7	chr2:96055000-96059600	Enhancers	Duodenum Mucosa	Duodenum
8	chr2:96055400-96057400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:96055400-96067200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:96055400-96067200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:96055400-96067200	Weak transcription	Brain Anterior Caudate	brain
12	chr2:96055600-96057800	Weak transcription	Adipose Nuclei	Adipose
13	chr2:96055600-96058600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:96055800-96057400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:96055800-96057800	Enhancers	Gastric	stomach
16	chr2:96055800-96058000	Flanking Active TSS	HepG2	liver
17	chr2:96055800-96059400	Enhancers	Fetal Heart	heart
18	chr2:96056200-96059600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr2:96056400-96057200	Weak transcription	Placenta	Placenta
20	chr2:96056400-96057400	Weak transcription	Colonic Mucosa	Colon
21	chr2:96056400-96057400	Weak transcription	Right Ventricle	heart
22	chr2:96056400-96057600	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr2:96056600-96058400	Enhancers	Ovary	ovary
24	chr2:96057000-96058000	Enhancers	Left Ventricle	heart

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