Variant report

Variant	rs7975161
Chromosome Location	chr12:104645405-104645406
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	chr12:104643349..104645898-chr12:104680595..104683102,2	K562	blood:
2	chr12:104643850..104647465-chr12:104679926..104684172,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EID3-2	chr12:104645305-104645456	NONHSAT030412
2	lnc-EID3-2	chr12:104645324-104645456	NONHSAT030413

Variant related genes	Relation type
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10400561	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10507174	0.85[CHB][hapmap]
rs10507175	0.85[CHB][hapmap];0.81[MEX][hapmap]
rs10735392	0.81[MEX][hapmap]
rs10745994	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10745995	0.85[CHB][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs10745996	0.85[CHB][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs10778311	0.81[JPT][hapmap]
rs10778316	0.88[JPT][hapmap]
rs10778318	0.81[JPT][hapmap]
rs10778323	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs10861169	1.00[JPT][hapmap]
rs10861180	0.90[JPT][hapmap]
rs10861181	0.96[EUR][1000 genomes]
rs11111898	0.85[CHB][hapmap]
rs11111943	0.98[ASN][1000 genomes]
rs11111946	0.82[AFR][1000 genomes]
rs11111955	0.80[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111960	0.81[JPT][hapmap]
rs11111963	0.81[JPT][hapmap]
rs12310731	0.95[AFR][1000 genomes]
rs12422505	0.85[CHB][hapmap]
rs12423844	0.85[CHB][hapmap]
rs12424869	0.88[JPT][hapmap]
rs12424943	0.85[CHB][hapmap]
rs12426862	0.85[CHB][hapmap]
rs12582966	0.85[CHB][hapmap]
rs12825521	0.85[CHB][hapmap]
rs17035297	0.87[ASW][hapmap]
rs17035324	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17192854	0.85[CHB][hapmap]
rs17805748	0.85[CHB][hapmap]
rs17805766	0.85[CHB][hapmap]
rs4129598	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[ASN][1000 genomes]
rs4131750	0.85[CHB][hapmap]
rs4131752	0.85[CHB][hapmap]
rs4246264	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4388968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4406890	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.96[EUR][1000 genomes]
rs4475991	0.89[JPT][hapmap]
rs4545635	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[ASN][1000 genomes]
rs4614534	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.93[MEX][hapmap]
rs4964257	0.98[ASN][1000 genomes]
rs4964260	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[ASN][1000 genomes]
rs4964267	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4964270	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964271	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4964288	0.81[MEX][hapmap]
rs4964627	1.00[CHB][hapmap]
rs4964728	1.00[CEU][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs4964735	0.81[JPT][hapmap]
rs4964741	0.84[ASN][1000 genomes]
rs4964752	0.81[JPT][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs4964761	0.81[JPT][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs4964779	0.81[MEX][hapmap]
rs6419386	0.89[ASN][1000 genomes]
rs6539128	0.91[ASN][1000 genomes]
rs6539132	0.89[EUR][1000 genomes]
rs6539138	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs7132418	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7138035	0.84[ASN][1000 genomes]
rs7138317	0.96[ASN][1000 genomes]
rs7138523	0.81[JPT][hapmap]
rs7294997	0.84[ASN][1000 genomes]
rs7295413	0.93[ASN][1000 genomes]
rs7297560	0.96[EUR][1000 genomes]
rs7299866	1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[MEX][hapmap]
rs7305872	0.93[ASN][1000 genomes]
rs7310505	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs7313063	0.89[JPT][hapmap]
rs7314893	0.84[JPT][hapmap]
rs7342395	0.81[JPT][hapmap]
rs7958851	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7960443	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7969351	0.82[ASN][1000 genomes]
rs7972034	0.81[ASN][1000 genomes]
rs7978101	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Toenail selenium levels	25343990	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7975161	C12orf48	cis	cerebellum	SCAN
rs7975161	CHST11	cis	parietal	SCAN
rs7975161	NR1H4	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104642000-104648600	Weak transcription	Hela-S3	cervix
2	chr12:104643000-104646600	Enhancers	A549	lung
3	chr12:104643000-104649000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:104643200-104646800	Weak transcription	K562	blood

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