Variant report

Variant	rs10888393
Chromosome Location	chr1:150745604-150745605
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:150543916..150546115-chr1:150744599..150746718,2	K562	blood:
2	chr1:150737960..150741233-chr1:150743077..150746063,3	K562	blood:

Variant related genes	Relation type
ENSG00000163131	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1027699	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10305664	0.85[EUR][1000 genomes]
rs10305672	0.88[EUR][1000 genomes]
rs10305673	0.90[EUR][1000 genomes]
rs10305704	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10305711	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10305714	0.90[EUR][1000 genomes]
rs10399947	0.82[EUR][1000 genomes]
rs10788794	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10888391	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10888392	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10888394	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10888395	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10888397	0.84[EUR][1000 genomes]
rs11204717	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11204718	0.82[AMR][1000 genomes]
rs11204722	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11204723	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204726	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204733	0.88[EUR][1000 genomes]
rs11204739	0.84[EUR][1000 genomes]
rs11204742	0.83[EUR][1000 genomes]
rs1134067	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1136808	0.81[AFR][1000 genomes]
rs11552229	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11581757	0.84[EUR][1000 genomes]
rs11582281	0.89[EUR][1000 genomes]
rs11587444	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11589458	0.90[EUR][1000 genomes]
rs11800855	0.83[EUR][1000 genomes]
rs12068264	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12085336	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12090215	0.84[EUR][1000 genomes]
rs12096831	0.85[EUR][1000 genomes]
rs12097963	0.84[EUR][1000 genomes]
rs12404949	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12409208	0.85[EUR][1000 genomes]
rs12410394	0.85[EUR][1000 genomes]
rs1415148	0.81[AFR][1000 genomes]
rs1532770	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16827671	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17660092	0.90[EUR][1000 genomes]
rs1889740	0.83[EUR][1000 genomes]
rs2089082	0.90[EUR][1000 genomes]
rs2228099	0.83[EUR][1000 genomes]
rs2230061	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2256355	0.83[EUR][1000 genomes]
rs2275235	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2864869	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2864871	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2864873	0.83[EUR][1000 genomes]
rs3754212	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768013	0.81[EUR][1000 genomes]
rs3768015	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3768016	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3768018	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4319334	0.83[EUR][1000 genomes]
rs4509581	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4537557	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4970928	0.80[EUR][1000 genomes]
rs4970929	0.82[EUR][1000 genomes]
rs4970930	0.83[EUR][1000 genomes]
rs4970982	0.85[EUR][1000 genomes]
rs57818453	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59337856	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6657388	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6660084	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6660845	0.87[EUR][1000 genomes]
rs6669855	0.82[EUR][1000 genomes]
rs6671737	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6693120	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72704603	0.81[AMR][1000 genomes]
rs72704639	0.85[EUR][1000 genomes]
rs72704652	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72704654	0.90[EUR][1000 genomes]
rs72704656	0.83[EUR][1000 genomes]
rs72704658	0.90[EUR][1000 genomes]
rs72704682	0.81[EUR][1000 genomes]
rs72704685	0.80[EUR][1000 genomes]
rs7418501	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7511673	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7514004	0.83[EUR][1000 genomes]
rs7521592	0.90[EUR][1000 genomes]
rs7521898	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7526489	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7532045	0.82[EUR][1000 genomes]
rs7540874	0.81[AFR][1000 genomes]
rs7556661	0.84[EUR][1000 genomes]
rs897815	0.83[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:24)

SNP	Gene	Cis/trans	Tissue	Source
rs10888393	RP11-316M1.12	cis	Whole Blood	GTEx
rs10888393	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs10888393	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs10888393	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs10888393	GOLPH3L	cis	Nerve Tibial	GTEx
rs10888393	HORMAD1	cis	Esophagus Mucosa	GTEx
rs10888393	CTSS	cis	Artery Tibial	GTEx
rs10888393	RP11-316M1.12	cis	lung	GTEx
rs10888393	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs10888393	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs10888393	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs10888393	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs10888393	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs10888393	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs10888393	RP11-316M1.12	cis	Thyroid	GTEx
rs10888393	HORMAD1	cis	Nerve Tibial	GTEx
rs10888393	RP11-316M1.12	cis	Artery Aorta	GTEx
rs10888393	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs10888393	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs10888393	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs10888393	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs10888393	CTSS	cis	Thyroid	GTEx
rs10888393	RP11-316M1.12	cis	Artery Tibial	GTEx
rs10888393	RP11-316M1.12	cis	Muscle Skeletal	GTEx

Chromatin state (count:7 , 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	chr1:150745000-150746200	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr1:150745200-150747200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr1:150745400-150745800	Weak transcription	NHDF-Ad	bronchial

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