Variant report

Variant	rs4950117
Chromosome Location	chr1:98490165-98490166
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 207 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:199)

rs_ID	r²[population]
rs10747488	0.82[JPT][hapmap]
rs10747489	0.85[JPT][hapmap]
rs10747491	1.00[JPT][hapmap]
rs10747492	1.00[JPT][hapmap]
rs10747495	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747496	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783082	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875112	1.00[JPT][hapmap]
rs10875113	1.00[JPT][hapmap]
rs10875118	1.00[JPT][hapmap]
rs10875121	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875125	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165920	1.00[JPT][hapmap]
rs11165921	1.00[JPT][hapmap]
rs11165934	0.85[ASN][1000 genomes]
rs11165935	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11165937	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11165938	0.85[ASN][1000 genomes]
rs11165939	0.85[ASN][1000 genomes]
rs11165940	0.85[ASN][1000 genomes]
rs1198571	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1198572	1.00[ASN][1000 genomes]
rs1198573	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1198574	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1198575	0.93[ASN][1000 genomes]
rs1198576	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1198577	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1198578	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1198579	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1198580	0.93[ASN][1000 genomes]
rs1198581	0.93[ASN][1000 genomes]
rs1198582	0.93[ASN][1000 genomes]
rs1198583	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1198588	0.93[ASN][1000 genomes]
rs1198589	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1198590	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1198591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1198592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1198593	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1198594	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1198596	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1198598	0.93[ASN][1000 genomes]
rs1198600	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12062845	1.00[JPT][hapmap]
rs12067567	0.85[ASN][1000 genomes]
rs12067700	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12068763	0.85[ASN][1000 genomes]
rs12069474	0.85[ASN][1000 genomes]
rs12071067	0.85[ASN][1000 genomes]
rs12077442	1.00[JPT][hapmap]
rs1211661	0.90[ASN][1000 genomes]
rs12406713	1.00[JPT][hapmap]
rs1622611	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1628294	1.00[ASN][1000 genomes]
rs1702291	0.93[ASN][1000 genomes]
rs1702292	0.93[ASN][1000 genomes]
rs1702293	1.00[ASN][1000 genomes]
rs1702294	1.00[ASN][1000 genomes]
rs17379561	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs1782810	1.00[ASN][1000 genomes]
rs1782811	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1782812	0.93[ASN][1000 genomes]
rs1782813	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1782815	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1782818	0.93[ASN][1000 genomes]
rs1801265	1.00[JPT][hapmap]
rs1892549	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892550	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892551	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892552	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938558	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938559	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938560	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938561	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938562	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938563	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1938564	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938565	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938566	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1938567	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938568	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938569	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938571	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938572	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938573	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2022864	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2022865	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2154402	1.00[ASN][1000 genomes]
rs2154403	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391873	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391902	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391903	1.00[ASN][1000 genomes]
rs2391904	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391905	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2660298	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2660299	0.93[ASN][1000 genomes]
rs2660300	0.93[ASN][1000 genomes]
rs2660301	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2660303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2660304	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs2802525	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2802529	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2802530	0.93[ASN][1000 genomes]
rs2802531	0.93[ASN][1000 genomes]
rs2802532	0.93[ASN][1000 genomes]
rs2802533	0.93[ASN][1000 genomes]
rs2802535	0.96[ASN][1000 genomes]
rs2802536	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28582591	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28641479	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2893376	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41285694	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4245673	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4246515	1.00[JPT][hapmap]
rs4246516	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4274102	0.81[ASN][1000 genomes]
rs4292998	1.00[ASN][1000 genomes]
rs4322261	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4372296	1.00[JPT][hapmap]
rs4378243	0.80[EUR][1000 genomes]
rs4379706	1.00[JPT][hapmap]
rs4394693	1.00[JPT][hapmap]
rs4394694	1.00[JPT][hapmap]
rs4411173	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4421623	0.82[JPT][hapmap]
rs4423049	1.00[JPT][hapmap]
rs4447033	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4456128	1.00[JPT][hapmap]
rs4477335	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4478846	0.81[EUR][1000 genomes]
rs4480407	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4506495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4523551	1.00[JPT][hapmap]
rs4523552	0.85[JPT][hapmap]
rs45522136	0.83[ASN][1000 genomes]
rs4573558	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4584446	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4598523	1.00[JPT][hapmap]
rs4634961	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4950118	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4950119	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4950120	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4970722	1.00[JPT][hapmap]
rs5005705	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56732321	0.85[ASN][1000 genomes]
rs57468345	0.85[ASN][1000 genomes]
rs61785881	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61785882	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61785883	0.90[ASN][1000 genomes]
rs61785886	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61785888	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61786696	0.93[ASN][1000 genomes]
rs61786697	0.93[ASN][1000 genomes]
rs61789075	0.90[ASN][1000 genomes]
rs61789077	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61789078	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61789079	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61789082	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6604093	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6664489	0.85[ASN][1000 genomes]
rs6677116	1.00[JPT][hapmap]
rs6692580	1.00[JPT][hapmap]
rs6703588	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs72963738	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7418577	1.00[JPT][hapmap]
rs7524038	1.00[JPT][hapmap]
rs7526108	0.82[JPT][hapmap]
rs9285628	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9324378	0.85[ASN][1000 genomes]
rs9324379	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9324380	1.00[ASN][1000 genomes]
rs9324381	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9324382	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9324383	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9324384	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9324385	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9324386	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9324387	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9324388	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9324389	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9440288	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9440293	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9440393	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9658841	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9659380	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9659624	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9659996	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9661157	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9661794	1.00[JPT][hapmap]
rs9662719	1.00[JPT][hapmap]
rs9662870	1.00[JPT][hapmap]
rs9724773	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9725319	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9727548	1.00[JPT][hapmap]
rs9727941	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9727976	1.00[JPT][hapmap]
rs9729190	0.85[ASN][1000 genomes]
rs9887831	0.85[ASN][1000 genomes]
rs9887848	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
4	nsv1009621	chr1:98435638-98599284	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
5	nsv871230	chr1:98436232-98564736	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
6	nsv470729	chr1:98461443-98564736	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
7	nsv546874	chr1:98461443-98564736	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
8	nsv830736	chr1:98488491-98663726	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4950117	HIAT1	cis	parietal	SCAN
rs4950117	SNX7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:98463800-98499800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:98475200-98492400	Weak transcription	NHDF-Ad	bronchial
3	chr1:98485400-98491600	Weak transcription	Osteobl	bone
4	chr1:98485600-98492600	Weak transcription	Hela-S3	cervix
5	chr1:98486200-98494200	Weak transcription	HUVEC	blood vessel
6	chr1:98487400-98501200	Weak transcription	HSMM	muscle
7	chr1:98488200-98498800	Weak transcription	Fetal Brain Female	brain
8	chr1:98489400-98491600	Enhancers	A549	lung

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