Variant report

Variant	rs12304982
Chromosome Location	chr12:9881099-9881100
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	chr12:9876110..9878240-chr12:9880296..9883371,3	K562	blood:
2	chr12:9874964..9878982-chr12:9880296..9882811,3	K562	blood:

Variant related genes	Relation type
ENSG00000184293	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10161013	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10492164	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs10743828	0.91[EUR][1000 genomes]
rs10772093	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10772099	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10844656	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs1134543	0.84[EUR][1000 genomes]
rs11835594	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12820281	0.95[EUR][1000 genomes]
rs12824727	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13377908	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13377939	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16914640	0.85[CEU][hapmap]
rs16923367	1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs16927874	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080210	0.83[EUR][1000 genomes]
rs2268145	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2401387	0.84[EUR][1000 genomes]
rs2401388	0.92[CEU][hapmap];0.90[GIH][hapmap];0.84[EUR][1000 genomes]
rs3176793	1.00[CHD][hapmap]
rs34584384	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34633868	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35990903	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3922289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611290	0.84[EUR][1000 genomes]
rs4763296	0.81[EUR][1000 genomes]
rs4763864	0.83[EUR][1000 genomes]
rs55715780	0.84[EUR][1000 genomes]
rs56980650	0.84[EUR][1000 genomes]
rs59016059	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59210706	0.84[EUR][1000 genomes]
rs6488120	0.82[EUR][1000 genomes]
rs6488121	0.82[EUR][1000 genomes]
rs6488123	1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs6488176	0.89[EUR][1000 genomes]
rs71447599	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71447600	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301386	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74062704	0.84[EUR][1000 genomes]
rs74062708	0.87[EUR][1000 genomes]
rs74065337	0.84[EUR][1000 genomes]
rs74065339	0.84[EUR][1000 genomes]
rs74065340	0.84[EUR][1000 genomes]
rs7962964	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964917	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967436	0.82[EUR][1000 genomes]
rs7969022	0.92[CEU][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes]
rs7976474	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12304982	C12orf53	cis	parietal	SCAN
rs12304982	RP11-75L1.2	cis	lung	GTEx
rs12304982	RP11-75L1.2	cis	Adipose Subcutaneous	GTEx
rs12304982	RP11-75L1.2	cis	Nerve Tibial	GTEx
rs12304982	RP11-75L1.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12304982	RP11-75L1.2	cis	Whole Blood	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9861600-9882400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:9864600-9883800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr12:9874400-9881400	Enhancers	Primary B cells from cord blood	blood
4	chr12:9875000-9881200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr12:9878600-9882600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr12:9878600-9886000	Active TSS	GM12878-XiMat	blood
7	chr12:9879200-9882800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr12:9881000-9884000	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links