Variant report

Variant	rs10161013
Chromosome Location	chr12:9884806-9884807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10492164	0.86[EUR][1000 genomes]
rs10743828	0.93[EUR][1000 genomes]
rs10772093	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772099	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10844656	0.94[EUR][1000 genomes]
rs11052306	0.80[EUR][1000 genomes]
rs1134543	0.86[EUR][1000 genomes]
rs11835594	1.00[EUR][1000 genomes]
rs12304982	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12820281	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12824727	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13377908	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13377939	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16923367	0.86[EUR][1000 genomes]
rs16927874	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2080210	0.85[EUR][1000 genomes]
rs2268145	0.98[EUR][1000 genomes]
rs2401387	0.86[EUR][1000 genomes]
rs2401388	0.86[EUR][1000 genomes]
rs3136576	0.80[EUR][1000 genomes]
rs34584384	0.95[EUR][1000 genomes]
rs34633868	0.97[EUR][1000 genomes]
rs35974438	1.00[ASN][1000 genomes]
rs35990903	1.00[EUR][1000 genomes]
rs3922289	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4611290	0.86[EUR][1000 genomes]
rs4763296	0.82[EUR][1000 genomes]
rs4763864	0.84[EUR][1000 genomes]
rs55715780	0.86[EUR][1000 genomes]
rs56980650	0.86[EUR][1000 genomes]
rs59016059	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59210706	0.86[EUR][1000 genomes]
rs6488110	0.81[EUR][1000 genomes]
rs6488120	0.84[EUR][1000 genomes]
rs6488121	0.84[EUR][1000 genomes]
rs6488123	0.84[EUR][1000 genomes]
rs6488176	0.91[EUR][1000 genomes]
rs71447599	0.99[EUR][1000 genomes]
rs71447600	1.00[EUR][1000 genomes]
rs7301386	1.00[EUR][1000 genomes]
rs74062704	0.86[EUR][1000 genomes]
rs74062708	0.89[EUR][1000 genomes]
rs74065337	0.86[EUR][1000 genomes]
rs74065339	0.86[EUR][1000 genomes]
rs74065340	0.86[EUR][1000 genomes]
rs7962964	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7964917	1.00[EUR][1000 genomes]
rs7967436	0.84[EUR][1000 genomes]
rs7969022	0.93[EUR][1000 genomes]
rs7976474	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv983235	chr12:9852218-9893776	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2757490	chr12:9855958-9888553	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10161013	RP11-75L1.2	cis	lung	GTEx
rs10161013	RP11-75L1.2	cis	Whole Blood	GTEx
rs10161013	RP11-75L1.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10161013	RP11-75L1.2	cis	Nerve Tibial	GTEx
rs10161013	RP11-75L1.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9878600-9886000	Active TSS	GM12878-XiMat	blood
2	chr12:9881600-9885600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr12:9883200-9886000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:9883400-9885200	Active TSS	Primary T cells fromperipheralblood	blood
5	chr12:9883400-9885800	Active TSS	Duodenum Mucosa	Duodenum
6	chr12:9883400-9886000	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr12:9883800-9885800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr12:9884000-9885000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:9884000-9886000	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr12:9884200-9885400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:9884400-9885000	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr12:9884400-9885200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:9884400-9885200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr12:9884400-9885600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr12:9884600-9885600	Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr12:9884800-9885400	Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr12:9884800-9886000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
18	chr12:9884800-9886000	Flanking Active TSS	Primary B cells from peripheral blood	blood
19	chr12:9884800-9886800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr12:9884800-9887200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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