Variant report

Variant	rs10888398
Chromosome Location	chr1:150886782-150886783
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150800480..150802144-chr1:150885516..150887920,2	MCF-7	breast:
2	chr1:150825294..150827430-chr1:150885825..150887706,2	MCF-7	breast:
3	chr1:150524437..150526621-chr1:150884840..150887292,2	K562	blood:

Variant related genes	Relation type
ENSG00000143382	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 38 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs1027699	0.84[EUR][1000 genomes]
rs10305664	0.83[EUR][1000 genomes]
rs10305672	0.82[EUR][1000 genomes]
rs10305673	0.84[EUR][1000 genomes]
rs10305704	0.88[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs10305711	0.84[CEU][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs10305714	0.87[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs10305720	0.86[EUR][1000 genomes]
rs10399947	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10788794	0.84[EUR][1000 genomes]
rs10888391	1.00[CEU][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs10888392	0.84[EUR][1000 genomes]
rs10888394	1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs10888395	0.88[EUR][1000 genomes]
rs10888397	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204722	0.96[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs11204726	1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs11204733	0.83[EUR][1000 genomes]
rs11204739	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204742	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204743	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11204747	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204748	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204749	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204750	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1136808	0.84[CEU][hapmap]
rs11552229	0.88[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs11581757	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11582281	0.83[EUR][1000 genomes]
rs11583707	0.82[ASN][1000 genomes]
rs11589458	0.84[EUR][1000 genomes]
rs11589886	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11800855	0.91[EUR][1000 genomes]
rs12059949	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12067685	0.82[ASN][1000 genomes]
rs12075597	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12085336	1.00[CEU][hapmap];0.82[GIH][hapmap];0.90[EUR][1000 genomes]
rs12086472	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs12089989	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs12090215	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12096831	0.82[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12097963	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12119409	0.90[CHB][hapmap]
rs12141871	0.90[CHB][hapmap]
rs12145224	0.91[CHB][hapmap]
rs12405726	0.81[ASN][1000 genomes]
rs12409208	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12410394	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12410869	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12562939	0.82[ASN][1000 genomes]
rs1415148	0.88[CEU][hapmap];0.80[TSI][hapmap]
rs1532770	0.82[EUR][1000 genomes]
rs1546376	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16827671	1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs17660092	0.84[EUR][1000 genomes]
rs1889740	1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs1889741	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1972060	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2004903	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2089082	0.84[EUR][1000 genomes]
rs2124952	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2228099	1.00[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2256355	1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2271076	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2272214	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2275235	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs2280627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2864873	1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2864882	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2867296	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2867297	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34985895	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36008098	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3738478	0.81[CHB][hapmap]
rs3768013	1.00[CEU][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs3768015	0.88[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs3768016	0.88[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs3768018	1.00[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs3843843	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3849279	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4319334	0.81[EUR][1000 genomes]
rs4451553	0.84[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4509581	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs4537557	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs4970928	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4970929	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4970930	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4970931	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4970980	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970982	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4970984	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4970985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4970986	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4970987	0.87[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4970988	0.88[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs59024312	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59337856	0.86[EUR][1000 genomes]
rs6587542	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6658066	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6660084	0.86[EUR][1000 genomes]
rs6660845	0.87[EUR][1000 genomes]
rs6664622	0.90[CHB][hapmap]
rs6669855	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6677420	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs66847267	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6686064	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72704652	0.84[EUR][1000 genomes]
rs72704654	0.84[EUR][1000 genomes]
rs72704656	0.91[EUR][1000 genomes]
rs72704658	0.84[EUR][1000 genomes]
rs72704679	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72704682	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72704685	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7418501	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs7514004	0.91[EUR][1000 genomes]
rs7518156	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7521592	0.84[EUR][1000 genomes]
rs752376	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7528773	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7532045	1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs7540874	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs7548516	0.86[CHB][hapmap]
rs7556451	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7556661	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8444	0.88[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs897815	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs951281	0.88[CEU][hapmap]
rs9661876	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[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	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	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
3	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
4	nsv1008496	chr1:150845827-150970656	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv947130	chr1:150878115-150899504	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:38)

SNP	Gene	Cis/trans	Tissue	Source
rs10888398	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs10888398	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs10888398	CTSK	cis	cerebellum	SCAN
rs10888398	HORMAD1	cis	parietal	SCAN
rs10888398	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs10888398	RP11-316M1.12	cis	Artery Aorta	GTEx
rs10888398	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs10888398	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs10888398	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs10888398	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs10888398	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs10888398	CTSS	cis	lymphoblastoid	seeQTL
rs10888398	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs10888398	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs10888398	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs10888398	HORMAD1	cis	Esophagus Mucosa	GTEx
rs10888398	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs10888398	HORMAD1	cis	Nerve Tibial	GTEx
rs10888398	RP11-316M1.12	cis	Whole Blood	GTEx
rs10888398	CTSS	cis	multi-tissue	Pritchard
rs10888398	GOLPH3L	cis	Nerve Tibial	GTEx
rs10888398	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs10888398	CTSK	cis	parietal	SCAN
rs10888398	RORC	cis	parietal	SCAN
rs10888398	PSMD4	cis	parietal	SCAN
rs10888398	RP11-316M1.12	cis	lung	GTEx
rs10888398	CTSS	cis	cerebellum	SCAN
rs10888398	CTSS	cis	Thyroid	GTEx
rs10888398	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs10888398	RP11-316M1.12	cis	Thyroid	GTEx
rs10888398	RP11-316M1.12	cis	Artery Tibial	GTEx
rs10888398	GNRHR2	cis	cerebellum	SCAN
rs10888398	ARNT	cis	parietal	SCAN
rs10888398	RP11-98D18.3	cis	Esophagus Mucosa	GTEx
rs10888398	HORMAD1	cis	cerebellum	SCAN
rs10888398	CTSS	cis	parietal	SCAN
rs10888398	HFE2	cis	parietal	SCAN
rs10888398	ARNT	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150879200-150898200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:150885400-150887200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:150885600-150887200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:150886400-150888000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:150886600-150888000	Enhancers	NHDF-Ad	bronchial

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