Variant report

Variant	rs12060830
Chromosome Location	chr1:149995979-149995980
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:149994846..149996547-chr1:149998372..149999923,2	K562	blood:
2	chr1:149970593..149972989-chr1:149993853..149996794,2	K562	blood:
3	chr1:149856343..149858353-chr1:149994074..149996091,2	K562	blood:
4	chr1:149993826..149996579-chr1:149996891..149998482,2	MCF-7	breast:
5	chr1:149856853..149859922-chr1:149994074..149998027,3	K562	blood:
6	chr1:149993912..149996492-chr1:149997463..150000045,2	MCF-7	breast:
7	chr1:149993032..149997672-chr1:150001811..150004898,5	K562	blood:

Variant related genes	Relation type
ENSG00000184678	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000184260	Chromatin interaction

Extended variants
information (count: 232 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:230)

rs_ID	r²[population]
rs1046332	1.00[GIH][hapmap];0.82[MEX][hapmap]
rs10494259	1.00[ASW][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];0.95[YRI][hapmap]
rs10494261	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[ASN][1000 genomes]
rs10494264	1.00[ASN][1000 genomes]
rs10494363	1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];1.00[ASN][1000 genomes]
rs10749674	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10888568	1.00[ASN][1000 genomes]
rs1105209	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11205307	1.00[ASN][1000 genomes]
rs11205308	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[ASN][1000 genomes]
rs11205313	0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs11205314	0.86[AFR][1000 genomes]
rs11205317	1.00[ASN][1000 genomes]
rs11205319	1.00[ASN][1000 genomes]
rs11205321	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11205326	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11205331	1.00[ASN][1000 genomes]
rs11205333	1.00[ASN][1000 genomes]
rs11576997	1.00[ASN][1000 genomes]
rs11577346	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11583720	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11584091	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11584354	1.00[ASN][1000 genomes]
rs11584606	1.00[ASN][1000 genomes]
rs11585955	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11587963	1.00[ASN][1000 genomes]
rs11588837	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11589585	1.00[ASN][1000 genomes]
rs11589801	1.00[ASN][1000 genomes]
rs11589922	1.00[ASN][1000 genomes]
rs11591200	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12022928	0.95[YRI][hapmap];0.90[AFR][1000 genomes]
rs12058090	1.00[ASN][1000 genomes]
rs12058502	1.00[ASN][1000 genomes]
rs12060027	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12060171	0.98[AFR][1000 genomes]
rs12060211	1.00[ASN][1000 genomes]
rs12061196	1.00[ASN][1000 genomes]
rs12061565	1.00[ASN][1000 genomes]
rs12061856	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12062861	1.00[ASN][1000 genomes]
rs12063059	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12063281	1.00[ASN][1000 genomes]
rs12063329	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12064434	0.95[YRI][hapmap]
rs12065681	1.00[ASN][1000 genomes]
rs12066132	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12066293	1.00[ASN][1000 genomes]
rs12067422	1.00[ASN][1000 genomes]
rs12073359	1.00[ASN][1000 genomes]
rs12074281	1.00[ASN][1000 genomes]
rs12077623	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12078573	1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];1.00[ASN][1000 genomes]
rs12081082	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12082035	1.00[ASW][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];0.95[YRI][hapmap]
rs12086155	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12087578	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs12091025	1.00[ASW][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs12091858	0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs12091904	0.80[AFR][1000 genomes]
rs12093499	1.00[ASN][1000 genomes]
rs12098106	1.00[ASN][1000 genomes]
rs12124898	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12138231	1.00[ASN][1000 genomes]
rs1339494	1.00[ASN][1000 genomes]
rs1339495	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1349532	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs1376676	1.00[GIH][hapmap]
rs1382573	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1545762	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs15931	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs16833063	1.00[ASW][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];0.86[YRI][hapmap]
rs16833149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16833175	1.00[ASW][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs16833178	0.92[ASW][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs16835135	1.00[GIH][hapmap];0.84[TSI][hapmap]
rs16835254	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16836630	1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];1.00[ASN][1000 genomes]
rs16838432	1.00[ASW][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];0.95[YRI][hapmap]
rs17581380	1.00[CHB][hapmap]
rs17643644	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[ASN][1000 genomes]
rs1804775	1.00[ASN][1000 genomes]
rs1824849	1.00[ASN][1000 genomes]
rs1824850	1.00[ASN][1000 genomes]
rs1964542	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1975957	1.00[ASN][1000 genomes]
rs2027349	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2039800	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2044891	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2198194	1.00[ASN][1000 genomes]
rs2279171	1.00[CHB][hapmap]
rs2318763	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2319280	1.00[ASN][1000 genomes]
rs28366567	1.00[ASN][1000 genomes]
rs28443768	1.00[ASN][1000 genomes]
rs28560140	1.00[ASN][1000 genomes]
rs28660389	1.00[ASN][1000 genomes]
rs28753817	1.00[ASN][1000 genomes]
rs3118119	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3208509	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs35230744	1.00[ASN][1000 genomes]
rs3850838	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3925724	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4058847	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs41264630	1.00[ASN][1000 genomes]
rs41265185	1.00[ASN][1000 genomes]
rs41302101	1.00[ASN][1000 genomes]
rs4279885	0.95[YRI][hapmap]
rs45548131	1.00[ASN][1000 genomes]
rs4926406	1.00[CHB][hapmap]
rs4926407	1.00[ASN][1000 genomes]
rs4926408	1.00[ASN][1000 genomes]
rs4926409	1.00[CHB][hapmap]
rs4926411	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4926412	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs55633125	1.00[ASN][1000 genomes]
rs55647342	1.00[ASN][1000 genomes]
rs55705001	1.00[ASN][1000 genomes]
rs55802315	1.00[ASN][1000 genomes]
rs55840680	1.00[ASN][1000 genomes]
rs55840906	1.00[ASN][1000 genomes]
rs55909733	1.00[ASN][1000 genomes]
rs55918911	1.00[ASN][1000 genomes]
rs55963510	1.00[ASN][1000 genomes]
rs56125600	1.00[ASN][1000 genomes]
rs56188926	1.00[ASN][1000 genomes]
rs56212907	1.00[ASN][1000 genomes]
rs56265028	1.00[ASN][1000 genomes]
rs56305459	1.00[ASN][1000 genomes]
rs56349882	1.00[ASN][1000 genomes]
rs56369603	1.00[ASN][1000 genomes]
rs56892994	1.00[ASN][1000 genomes]
rs58342123	0.98[AFR][1000 genomes]
rs58395667	1.00[ASN][1000 genomes]
rs58426216	1.00[ASN][1000 genomes]
rs59054339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59607464	1.00[ASN][1000 genomes]
rs6657062	1.00[ASN][1000 genomes]
rs66649150	1.00[ASN][1000 genomes]
rs6666959	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6687454	1.00[ASN][1000 genomes]
rs67450539	1.00[ASN][1000 genomes]
rs67880399	1.00[ASN][1000 genomes]
rs68144650	1.00[ASN][1000 genomes]
rs72692803	1.00[ASN][1000 genomes]
rs72692804	1.00[ASN][1000 genomes]
rs72692805	1.00[ASN][1000 genomes]
rs72692807	1.00[ASN][1000 genomes]
rs72692808	1.00[ASN][1000 genomes]
rs72692810	1.00[ASN][1000 genomes]
rs72692811	1.00[ASN][1000 genomes]
rs72692812	1.00[ASN][1000 genomes]
rs72692813	1.00[ASN][1000 genomes]
rs72692814	1.00[ASN][1000 genomes]
rs72692816	1.00[ASN][1000 genomes]
rs72692818	1.00[ASN][1000 genomes]
rs72692819	1.00[ASN][1000 genomes]
rs72692834	1.00[ASN][1000 genomes]
rs72692835	1.00[ASN][1000 genomes]
rs72692837	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692840	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692842	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692843	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692849	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692851	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692854	1.00[ASN][1000 genomes]
rs72692857	1.00[ASN][1000 genomes]
rs72692861	1.00[ASN][1000 genomes]
rs72692862	1.00[ASN][1000 genomes]
rs72692865	1.00[ASN][1000 genomes]
rs72692866	1.00[ASN][1000 genomes]
rs72692869	1.00[ASN][1000 genomes]
rs72692886	1.00[ASN][1000 genomes]
rs72692893	1.00[ASN][1000 genomes]
rs72692895	1.00[ASN][1000 genomes]
rs72692896	1.00[ASN][1000 genomes]
rs72692897	1.00[ASN][1000 genomes]
rs72692898	1.00[ASN][1000 genomes]
rs72692899	1.00[ASN][1000 genomes]
rs72692900	1.00[ASN][1000 genomes]
rs72692901	1.00[ASN][1000 genomes]
rs72694905	1.00[ASN][1000 genomes]
rs72694906	1.00[ASN][1000 genomes]
rs72694908	1.00[ASN][1000 genomes]
rs72694914	1.00[ASN][1000 genomes]
rs72694915	1.00[ASN][1000 genomes]
rs72694917	1.00[ASN][1000 genomes]
rs72694918	1.00[ASN][1000 genomes]
rs72694919	1.00[ASN][1000 genomes]
rs72694923	1.00[ASN][1000 genomes]
rs72694926	1.00[ASN][1000 genomes]
rs72694927	1.00[ASN][1000 genomes]
rs72694928	1.00[ASN][1000 genomes]
rs72694933	1.00[ASN][1000 genomes]
rs72694936	1.00[ASN][1000 genomes]
rs72694942	1.00[ASN][1000 genomes]
rs72694944	1.00[ASN][1000 genomes]
rs72694945	1.00[ASN][1000 genomes]
rs72694946	1.00[ASN][1000 genomes]
rs72694950	1.00[ASN][1000 genomes]
rs72694951	1.00[ASN][1000 genomes]
rs72694953	1.00[ASN][1000 genomes]
rs72694956	1.00[ASN][1000 genomes]
rs72694957	1.00[ASN][1000 genomes]
rs72694959	1.00[ASN][1000 genomes]
rs72694960	1.00[ASN][1000 genomes]
rs72694961	1.00[ASN][1000 genomes]
rs72694962	1.00[ASN][1000 genomes]
rs72694964	1.00[ASN][1000 genomes]
rs72694965	1.00[ASN][1000 genomes]
rs72694969	1.00[ASN][1000 genomes]
rs72694974	1.00[ASN][1000 genomes]
rs72708162	1.00[ASN][1000 genomes]
rs73008195	1.00[ASN][1000 genomes]
rs74126211	0.88[AFR][1000 genomes]
rs7519918	1.00[ASN][1000 genomes]
rs7520930	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7521768	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7521783	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7530922	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7532876	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7540847	1.00[ASN][1000 genomes]
rs7544531	1.00[CHB][hapmap];1.00[GIH][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs7550323	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7550350	1.00[CHB][hapmap]
rs7553622	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7554367	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9662055	1.00[ASN][1000 genomes]
rs9804143	0.85[ASW][hapmap];0.83[MKK][hapmap];0.95[YRI][hapmap]
rs9988489	1.00[ASW][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831537	chr1:149833357-150064655	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	431 gene(s)	inside rSNPs	diseases
2	nsv8369	chr1:149995017-149996688	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12060830	FCGR1A	cis	multi-tissue	Pritchard
rs12060830	FCGR1C	cis	Whole Blood	GTEx
rs12060830	HIST2H4	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:149985600-150022000	Weak transcription	Brain Substantia Nigra	brain
2	chr1:149989600-149997800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:149989600-149998000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:149990600-149998000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:149991000-149996000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:149993800-150005400	Weak transcription	Fetal Heart	heart
7	chr1:149994200-149997200	Weak transcription	Liver	Liver
8	chr1:149995000-149996800	Weak transcription	Stomach Mucosa	stomach

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