Variant report

Variant	rs7975956
Chromosome Location	chr12:48635218-48635219
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10082861	0.86[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs1021313	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10219623	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs10431526	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10437919	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10437920	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10467101	0.94[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10783234	0.81[ASN][1000 genomes]
rs10875732	0.92[JPT][hapmap]
rs10875745	0.83[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs10875746	0.84[CHD][hapmap];0.93[JPT][hapmap]
rs10875750	0.83[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs10875762	0.83[ASN][1000 genomes]
rs10875764	0.80[ASN][1000 genomes]
rs10875767	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[ASN][1000 genomes]
rs10875768	0.91[ASN][1000 genomes]
rs10875769	0.89[ASN][1000 genomes]
rs10875770	0.86[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[YRI][hapmap];0.93[ASN][1000 genomes]
rs10875772	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10875777	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10875778	0.97[ASN][1000 genomes]
rs10875779	0.97[ASN][1000 genomes]
rs10875782	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875792	0.93[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs10875793	0.88[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs11168371	0.81[CHD][hapmap];0.93[JPT][hapmap]
rs11168403	0.93[JPT][hapmap]
rs11168413	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs11168414	0.83[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs11168418	0.83[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs11168420	0.88[CHD][hapmap];0.93[JPT][hapmap]
rs11168421	0.87[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.93[JPT][hapmap]
rs11168425	0.87[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs11168427	0.83[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs11168433	0.83[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs11168450	0.94[CHD][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs11168459	0.86[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[YRI][hapmap];0.93[ASN][1000 genomes]
rs11168483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168487	0.97[ASN][1000 genomes]
rs11168493	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168508	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11168510	0.91[ASN][1000 genomes]
rs11168514	0.90[ASN][1000 genomes]
rs11168516	0.88[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs11558768	0.82[ASN][1000 genomes]
rs12227601	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12297470	0.83[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs12300647	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304476	0.93[JPT][hapmap]
rs12305511	0.83[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs12305647	0.85[ASN][1000 genomes]
rs12306451	0.93[JPT][hapmap]
rs12310813	0.83[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs12312134	0.81[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs12317751	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12318705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471997	0.82[CHB][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap]
rs17122666	0.84[CHD][hapmap];0.93[JPT][hapmap]
rs17122812	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1859445	0.88[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs2012773	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs2054903	0.82[CHB][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap]
rs2107638	0.93[JPT][hapmap]
rs2171642	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2228500	0.83[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2269933	0.83[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs2269935	0.83[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap]
rs2279464	0.87[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2409005	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2634675	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs2732439	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs2732465	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs2898065	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2898066	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3185921	0.82[CHB][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap]
rs3751273	0.82[CHB][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap]
rs3782910	0.93[JPT][hapmap]
rs4760619	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs4760622	0.83[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs4760625	0.92[ASN][1000 genomes]
rs4760681	0.83[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap]
rs4760687	0.87[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs4760695	0.83[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs4760696	0.94[CHD][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs4760697	0.94[CHD][hapmap];0.93[JPT][hapmap]
rs4760699	0.95[ASN][1000 genomes]
rs61940962	0.93[ASN][1000 genomes]
rs61941003	0.97[ASN][1000 genomes]
rs61941006	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6580659	0.92[JPT][hapmap]
rs7135779	0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs716553	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs725454	0.84[CHD][hapmap];0.93[JPT][hapmap]
rs7297298	0.92[ASN][1000 genomes]
rs7302466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303055	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7486008	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7486424	0.87[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap]
rs8804	0.83[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs886588	0.93[JPT][hapmap]
rs9634261	0.88[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs989144	0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7975956	RND1	cis	cerebellum	SCAN
rs7975956	C12orf41	cis	parietal	SCAN
rs7975956	H1FNT	cis	parietal	SCAN
rs7975956	FBXL12	trans	cerebellum	SCAN
rs7975956	RPAP3	cis	cerebellum	SCAN
rs7975956	LMBR1L	cis	parietal	SCAN
rs7975956	AQP6	cis	parietal	SCAN
rs7975956	RP1-228P16.1	cis	Thyroid	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48612200-48635600	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:48630600-48636600	Weak transcription	Primary monocytes fromperipheralblood	blood

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