Variant report

Variant	rs4378243
Chromosome Location	chr1:98395881-98395882
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:98386898..98389575-chr1:98395488..98397277,2	K562	blood:

Extended variants
information (count: 171 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:166)

rs_ID	r²[population]
rs10747488	0.82[JPT][hapmap]
rs10747489	0.85[JPT][hapmap]
rs10747490	0.82[ASN][1000 genomes]
rs10747491	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10747492	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10747495	0.80[EUR][1000 genomes]
rs10747496	0.80[EUR][1000 genomes]
rs10783082	0.80[EUR][1000 genomes]
rs10875111	0.82[ASN][1000 genomes]
rs10875112	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10875113	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10875118	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10875120	0.94[ASN][1000 genomes]
rs10875121	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11165920	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11165921	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11165934	0.82[ASN][1000 genomes]
rs11165935	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11165937	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11165938	0.82[ASN][1000 genomes]
rs11165939	0.82[ASN][1000 genomes]
rs11165940	0.82[ASN][1000 genomes]
rs1198571	0.80[EUR][1000 genomes]
rs1198573	0.80[EUR][1000 genomes]
rs1198574	0.80[EUR][1000 genomes]
rs1198591	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1198592	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1198593	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1198594	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12062845	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12067567	0.82[ASN][1000 genomes]
rs12067700	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12068763	0.82[ASN][1000 genomes]
rs12069474	0.82[ASN][1000 genomes]
rs12071067	0.82[ASN][1000 genomes]
rs12077442	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12406713	0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17379561	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1782811	0.80[EUR][1000 genomes]
rs1782813	0.80[EUR][1000 genomes]
rs1782815	0.80[EUR][1000 genomes]
rs1801265	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1892549	0.80[EUR][1000 genomes]
rs1892550	0.80[EUR][1000 genomes]
rs1892551	0.80[EUR][1000 genomes]
rs1892552	0.80[EUR][1000 genomes]
rs1938558	0.80[EUR][1000 genomes]
rs1938559	0.80[EUR][1000 genomes]
rs1938560	0.80[EUR][1000 genomes]
rs1938561	0.80[EUR][1000 genomes]
rs1938562	0.80[EUR][1000 genomes]
rs1938563	0.80[EUR][1000 genomes]
rs1938564	0.81[EUR][1000 genomes]
rs1938565	0.80[EUR][1000 genomes]
rs1938567	0.80[EUR][1000 genomes]
rs1938568	0.80[EUR][1000 genomes]
rs1938569	0.80[EUR][1000 genomes]
rs2154403	0.84[EUR][1000 genomes]
rs2391873	0.83[EUR][1000 genomes]
rs2391902	0.81[EUR][1000 genomes]
rs2391904	0.80[EUR][1000 genomes]
rs2391905	0.80[EUR][1000 genomes]
rs2660303	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2660304	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs28582591	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28641479	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2893376	0.83[EUR][1000 genomes]
rs41285694	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4245673	0.80[EUR][1000 genomes]
rs4246515	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4246516	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4294451	0.94[ASN][1000 genomes]
rs4322261	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4372296	1.00[JPT][hapmap]
rs4379706	1.00[JPT][hapmap]
rs4394693	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4394694	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4399192	0.88[ASN][1000 genomes]
rs4411173	0.80[EUR][1000 genomes]
rs4421623	0.82[JPT][hapmap]
rs4423049	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4447033	0.80[EUR][1000 genomes]
rs4456128	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4477335	0.80[EUR][1000 genomes]
rs4478846	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4495746	0.85[ASN][1000 genomes]
rs4506495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4523551	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4523552	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs45522136	0.81[ASN][1000 genomes]
rs4573558	0.84[EUR][1000 genomes]
rs4584446	0.80[EUR][1000 genomes]
rs4598523	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4634961	0.80[EUR][1000 genomes]
rs4950117	0.80[EUR][1000 genomes]
rs4950118	0.80[EUR][1000 genomes]
rs4950120	0.80[EUR][1000 genomes]
rs4970720	0.82[ASN][1000 genomes]
rs4970721	0.82[ASN][1000 genomes]
rs4970722	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4970723	0.82[ASN][1000 genomes]
rs4970725	0.94[ASN][1000 genomes]
rs56732321	0.82[ASN][1000 genomes]
rs57468345	0.82[ASN][1000 genomes]
rs61785881	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61785882	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61785883	0.88[ASN][1000 genomes]
rs61785886	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61785888	0.84[EUR][1000 genomes]
rs61787783	0.87[ASN][1000 genomes]
rs61787784	0.87[ASN][1000 genomes]
rs61787785	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61787819	0.82[ASN][1000 genomes]
rs61787820	0.82[ASN][1000 genomes]
rs61787823	0.82[ASN][1000 genomes]
rs61787824	0.94[ASN][1000 genomes]
rs61787826	0.88[ASN][1000 genomes]
rs61787827	0.94[ASN][1000 genomes]
rs61787828	0.94[ASN][1000 genomes]
rs61787829	1.00[ASN][1000 genomes]
rs61787830	1.00[ASN][1000 genomes]
rs61789075	0.88[ASN][1000 genomes]
rs61789077	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61789078	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61789079	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61789082	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6604093	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6604098	0.88[ASN][1000 genomes]
rs6664489	0.82[ASN][1000 genomes]
rs6677116	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6692580	1.00[JPT][hapmap]
rs6703588	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs72963738	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7415086	0.94[ASN][1000 genomes]
rs7418577	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7524038	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7526108	0.82[JPT][hapmap]
rs9285628	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9324374	0.82[ASN][1000 genomes]
rs9324378	0.82[ASN][1000 genomes]
rs9324379	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9324383	0.80[EUR][1000 genomes]
rs9324384	0.80[EUR][1000 genomes]
rs9324385	0.80[EUR][1000 genomes]
rs9324386	0.80[EUR][1000 genomes]
rs9324387	0.80[EUR][1000 genomes]
rs9324388	0.80[EUR][1000 genomes]
rs9324389	0.80[EUR][1000 genomes]
rs9440288	0.83[EUR][1000 genomes]
rs9440393	0.80[EUR][1000 genomes]
rs9658841	0.80[EUR][1000 genomes]
rs9659380	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9659624	0.80[EUR][1000 genomes]
rs9659996	0.80[EUR][1000 genomes]
rs9661157	0.80[EUR][1000 genomes]
rs9661794	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9662232	0.94[ASN][1000 genomes]
rs9662719	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9662870	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9725319	0.80[EUR][1000 genomes]
rs9727548	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9727976	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9729190	0.82[ASN][1000 genomes]
rs9729897	0.94[ASN][1000 genomes]
rs9887831	0.82[ASN][1000 genomes]
rs9887848	0.82[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	nsv1012958	chr1:98081528-98864746	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv871625	chr1:98165091-98564736	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830725	chr1:98257894-98443497	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv934244	chr1:98260729-98415915	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv871077	chr1:98274132-98541677	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4378243	HIAT1	cis	parietal	SCAN
rs4378243	SNX7	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:98391000-98402200	Weak transcription	Brain Anterior Caudate	brain
2	chr1:98391200-98402600	Weak transcription	HSMM	muscle
3	chr1:98395600-98396600	Enhancers	Fetal Brain Male	brain
4	chr1:98395800-98396400	Enhancers	HepG2	liver
5	chr1:98395800-98396800	Flanking Active TSS	Liver	Liver

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