Variant report

Variant	rs6693120
Chromosome Location	chr1:150748374-150748375
allele	C/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	chr1:150748050..150749658-chr1:150951794..150953371,2	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1027699	0.87[EUR][1000 genomes]
rs10305664	0.82[EUR][1000 genomes]
rs10305672	0.85[EUR][1000 genomes]
rs10305673	0.87[EUR][1000 genomes]
rs10305704	0.87[EUR][1000 genomes]
rs10305711	0.87[EUR][1000 genomes]
rs10305714	0.87[EUR][1000 genomes]
rs10788794	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10888391	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10888392	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10888393	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10888394	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888395	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10888397	0.81[EUR][1000 genomes]
rs11204696	0.80[ASN][1000 genomes]
rs11204713	0.81[ASN][1000 genomes]
rs11204717	0.83[ASN][1000 genomes]
rs11204718	0.81[ASN][1000 genomes]
rs11204722	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204723	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204726	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204733	0.85[EUR][1000 genomes]
rs11204739	0.81[EUR][1000 genomes]
rs1134067	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1136808	0.83[ASN][1000 genomes]
rs11552229	0.87[EUR][1000 genomes]
rs11581757	0.81[EUR][1000 genomes]
rs11582281	0.86[EUR][1000 genomes]
rs11584184	0.82[ASN][1000 genomes]
rs11584575	0.82[ASN][1000 genomes]
rs11587444	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11589458	0.87[EUR][1000 genomes]
rs12068264	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12085336	0.80[EUR][1000 genomes]
rs12086472	0.82[ASN][1000 genomes]
rs12089989	0.82[ASN][1000 genomes]
rs12090215	0.81[EUR][1000 genomes]
rs12096831	0.82[EUR][1000 genomes]
rs12097963	0.81[EUR][1000 genomes]
rs12404949	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12409208	0.82[EUR][1000 genomes]
rs12410394	0.82[EUR][1000 genomes]
rs1415148	0.83[ASN][1000 genomes]
rs1532770	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16827671	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17660092	0.87[EUR][1000 genomes]
rs2089082	0.87[EUR][1000 genomes]
rs2230061	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2275235	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2864869	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2864871	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35111350	0.82[ASN][1000 genomes]
rs3754212	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3768015	0.87[EUR][1000 genomes]
rs3768016	0.87[EUR][1000 genomes]
rs3768018	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4319334	0.83[ASN][1000 genomes]
rs4509581	0.83[ASN][1000 genomes]
rs4537557	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4970930	0.80[EUR][1000 genomes]
rs4970982	0.82[EUR][1000 genomes]
rs57818453	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59337856	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6657388	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6660084	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6660845	0.84[EUR][1000 genomes]
rs6671737	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6681990	0.82[ASN][1000 genomes]
rs6692960	0.82[ASN][1000 genomes]
rs72702585	0.82[ASN][1000 genomes]
rs72704603	0.83[ASN][1000 genomes]
rs72704639	0.81[EUR][1000 genomes]
rs72704652	0.87[EUR][1000 genomes]
rs72704654	0.87[EUR][1000 genomes]
rs72704658	0.86[EUR][1000 genomes]
rs7418501	0.83[ASN][1000 genomes]
rs7511673	0.83[ASN][1000 genomes]
rs7521592	0.87[EUR][1000 genomes]
rs7521898	0.83[ASN][1000 genomes]
rs7526489	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7533678	0.82[ASN][1000 genomes]
rs7540874	0.83[ASN][1000 genomes]
rs7556661	0.81[EUR][1000 genomes]
rs897815	0.80[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:23)

SNP	Gene	Cis/trans	Tissue	Source
rs6693120	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs6693120	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs6693120	RP11-316M1.12	cis	Artery Aorta	GTEx
rs6693120	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs6693120	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs6693120	CTSS	cis	Thyroid	GTEx
rs6693120	RP11-316M1.12	cis	Thyroid	GTEx
rs6693120	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs6693120	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs6693120	HORMAD1	cis	Nerve Tibial	GTEx
rs6693120	GOLPH3L	cis	Nerve Tibial	GTEx
rs6693120	RP11-316M1.12	cis	lung	GTEx
rs6693120	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs6693120	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs6693120	RP11-316M1.12	cis	Artery Tibial	GTEx
rs6693120	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs6693120	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs6693120	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs6693120	HORMAD1	cis	Esophagus Mucosa	GTEx
rs6693120	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs6693120	RP11-316M1.12	cis	Whole Blood	GTEx
rs6693120	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs6693120	ARNT	Cis_1M	lymphoblastoid	RTeQTL

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	chr1:150746800-150753400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:150747200-150750200	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr1:150748000-150748600	Enhancers	Monocytes-CD14+_RO01746	blood

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