Variant report

Variant	rs59337856
Chromosome Location	chr1:150746406-150746407
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150724802..150727328-chr1:150746278..150749231,2	MCF-7	breast:
2	chr1:150743215..150744968-chr1:150746292..150748650,2	MCF-7	breast:
3	chr1:150543916..150546115-chr1:150744599..150746718,2	K562	blood:

Extended variants
information (count: 107 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1027699	0.84[EUR][1000 genomes]
rs10305672	0.81[EUR][1000 genomes]
rs10305673	0.84[EUR][1000 genomes]
rs10305704	0.84[EUR][1000 genomes]
rs10305711	0.84[EUR][1000 genomes]
rs10305714	0.84[EUR][1000 genomes]
rs10305720	0.86[EUR][1000 genomes]
rs10399947	0.81[EUR][1000 genomes]
rs10788794	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10888391	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10888392	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10888393	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10888394	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888395	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10888398	0.86[EUR][1000 genomes]
rs11204713	0.81[ASN][1000 genomes]
rs11204717	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11204718	0.81[ASN][1000 genomes]
rs11204722	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204723	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204726	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204733	0.81[EUR][1000 genomes]
rs1134067	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1136808	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11552229	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11582281	0.83[EUR][1000 genomes]
rs11584184	0.82[ASN][1000 genomes]
rs11584575	0.82[ASN][1000 genomes]
rs11587444	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11589458	0.84[EUR][1000 genomes]
rs11589886	0.82[EUR][1000 genomes]
rs11800855	0.90[EUR][1000 genomes]
rs12068264	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12075597	0.83[EUR][1000 genomes]
rs12085336	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12086472	0.82[ASN][1000 genomes]
rs12089989	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12404949	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12410869	0.85[EUR][1000 genomes]
rs1415148	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1532770	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16827671	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17660092	0.84[EUR][1000 genomes]
rs1889740	0.90[EUR][1000 genomes]
rs1889741	0.84[EUR][1000 genomes]
rs1972060	0.81[EUR][1000 genomes]
rs2089082	0.84[EUR][1000 genomes]
rs2228099	0.90[EUR][1000 genomes]
rs2230061	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2256355	0.90[EUR][1000 genomes]
rs2271076	0.81[EUR][1000 genomes]
rs2275235	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2280627	0.81[EUR][1000 genomes]
rs2864869	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2864871	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2864873	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2864882	0.86[EUR][1000 genomes]
rs2867297	0.80[EUR][1000 genomes]
rs35111350	0.82[ASN][1000 genomes]
rs36008098	0.84[EUR][1000 genomes]
rs3754212	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768013	0.89[EUR][1000 genomes]
rs3768015	0.84[EUR][1000 genomes]
rs3768016	0.84[EUR][1000 genomes]
rs3768018	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4319334	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4509581	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4537557	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4970931	0.81[EUR][1000 genomes]
rs4970980	0.85[EUR][1000 genomes]
rs4970984	0.86[EUR][1000 genomes]
rs4970985	0.86[EUR][1000 genomes]
rs57818453	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6587542	0.81[EUR][1000 genomes]
rs6657388	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6660084	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6660845	0.81[EUR][1000 genomes]
rs6669855	0.81[EUR][1000 genomes]
rs6671737	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6681990	0.82[ASN][1000 genomes]
rs66847267	0.86[EUR][1000 genomes]
rs6686064	0.80[EUR][1000 genomes]
rs6692960	0.82[ASN][1000 genomes]
rs6693120	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72702585	0.82[ASN][1000 genomes]
rs72704603	0.83[ASN][1000 genomes]
rs72704652	0.84[EUR][1000 genomes]
rs72704654	0.84[EUR][1000 genomes]
rs72704656	0.90[EUR][1000 genomes]
rs72704658	0.83[EUR][1000 genomes]
rs72704679	0.84[EUR][1000 genomes]
rs7418501	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7511673	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7514004	0.90[EUR][1000 genomes]
rs7521592	0.84[EUR][1000 genomes]
rs7521898	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7526489	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7532045	0.89[EUR][1000 genomes]
rs7533678	0.82[ASN][1000 genomes]
rs7540874	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9661876	0.81[EUR][1000 genomes]

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	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv872417	chr1:150618632-150759979	Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv437169	chr1:150738197-150816886	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
6	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs59337856	RP11-316M1.12	cis	Artery Aorta	GTEx
rs59337856	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs59337856	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs59337856	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs59337856	RP11-316M1.12	cis	Thyroid	GTEx
rs59337856	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs59337856	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs59337856	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs59337856	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs59337856	HORMAD1	cis	Nerve Tibial	GTEx
rs59337856	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs59337856	CTSS	cis	Thyroid	GTEx
rs59337856	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs59337856	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs59337856	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs59337856	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs59337856	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs59337856	CTSS	cis	Artery Tibial	GTEx
rs59337856	GOLPH3L	cis	Nerve Tibial	GTEx
rs59337856	HORMAD1	cis	Esophagus Mucosa	GTEx
rs59337856	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs59337856	RP11-316M1.12	cis	Whole Blood	GTEx
rs59337856	RP11-316M1.12	cis	lung	GTEx
rs59337856	RP11-316M1.12	cis	Artery Tibial	GTEx
rs59337856	CTSS	cis	multi-tissue	Pritchard

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150737200-150761800	Weak transcription	Spleen	Spleen
2	chr1:150744200-150749800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:150744600-150768200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:150744800-150746800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr1:150745200-150747200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:150746200-150747400	Enhancers	Monocytes-CD14+_RO01746	blood

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