Variant report

Variant	rs1889741
Chromosome Location	chr1:150869045-150869046
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150865101..150868127-chr1:150868317..150870783,3	K562	blood:
2	chr1:150538508..150540794-chr1:150868102..150869659,2	K562	blood:
3	chr1:150867829..150869388-chr1:150873614..150875595,2	MCF-7	breast:
4	chr1:150859611..150863685-chr1:150866729..150869931,3	K562	blood:
5	chr1:150848907..150850900-chr1:150866879..150869881,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264508	Chromatin interaction
ENSG00000143437	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 42 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs1027699	0.85[EUR][1000 genomes]
rs10305664	0.85[EUR][1000 genomes]
rs10305672	0.83[EUR][1000 genomes]
rs10305673	0.85[EUR][1000 genomes]
rs10305704	0.88[CEU][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs10305711	0.84[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs10305714	0.87[CEU][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs10305720	0.88[EUR][1000 genomes]
rs10399947	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10788794	0.81[EUR][1000 genomes]
rs10888391	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs10888392	0.82[EUR][1000 genomes]
rs10888394	1.00[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs10888395	0.86[EUR][1000 genomes]
rs10888397	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];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10888398	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]
rs11204704	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs11204722	0.96[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs11204726	1.00[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs11204733	0.84[EUR][1000 genomes]
rs11204739	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204742	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204743	0.92[ASN][1000 genomes]
rs11204747	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204748	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204749	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204750	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1136808	0.84[CEU][hapmap]
rs11552229	0.88[CEU][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs11581757	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];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11582281	0.84[EUR][1000 genomes]
rs11586422	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs11589458	0.85[EUR][1000 genomes]
rs11589886	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11800855	0.93[EUR][1000 genomes]
rs11804276	0.88[CEU][hapmap]
rs11807409	0.88[CEU][hapmap]
rs12059949	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12063547	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs12072339	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs12075597	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12085336	1.00[CEU][hapmap];0.88[GIH][hapmap];0.92[EUR][1000 genomes]
rs12086472	0.88[CEU][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap]
rs12089989	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs12090215	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12096831	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12097963	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12119409	0.85[CHB][hapmap]
rs12141871	0.86[CHB][hapmap]
rs12145224	0.86[CHB][hapmap]
rs12409208	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12410394	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12410869	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[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];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1415148	0.88[CEU][hapmap];0.82[GIH][hapmap];0.80[TSI][hapmap]
rs1532770	0.80[EUR][1000 genomes]
rs1546376	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16827671	1.00[CEU][hapmap];0.88[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs17658705	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs17660092	0.85[EUR][1000 genomes]
rs1889740	1.00[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs1972060	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2004903	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2089082	0.85[EUR][1000 genomes]
rs2124952	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2228099	1.00[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs2256355	1.00[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs2271076	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2272214	0.88[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2275235	0.84[CEU][hapmap];0.86[GIH][hapmap];0.81[TSI][hapmap]
rs2275236	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs2280627	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2864873	1.00[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs2864882	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2867296	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2867297	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34985895	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36008098	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3768013	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs3768015	0.88[CEU][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs3768016	0.88[CEU][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs3768018	1.00[CEU][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs3843843	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3849279	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[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];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4451553	0.84[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs4509581	0.95[CEU][hapmap]
rs4537557	0.88[CEU][hapmap];0.86[GIH][hapmap];0.81[TSI][hapmap]
rs4970928	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4970929	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970930	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970931	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970980	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4970982	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4970984	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4970985	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4970986	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970987	0.87[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs4970988	0.88[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs59024312	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59337856	0.84[EUR][1000 genomes]
rs6587542	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6658066	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6660084	0.84[EUR][1000 genomes]
rs6660845	0.88[EUR][1000 genomes]
rs6664622	0.86[CHB][hapmap]
rs6669855	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6677420	0.84[ASN][1000 genomes]
rs66847267	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6686064	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72704652	0.85[EUR][1000 genomes]
rs72704654	0.85[EUR][1000 genomes]
rs72704656	0.93[EUR][1000 genomes]
rs72704658	0.85[EUR][1000 genomes]
rs72704679	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72704682	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72704685	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7418501	0.88[CEU][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap]
rs7514004	0.93[EUR][1000 genomes]
rs7518156	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7521592	0.85[EUR][1000 genomes]
rs752376	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[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];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7528773	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7532045	1.00[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs7540874	0.88[CEU][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap]
rs7548516	0.82[CHB][hapmap]
rs7556451	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7556661	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8444	0.88[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs897815	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];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs951281	0.88[CEU][hapmap]
rs9661876	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[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	nsv2810	chr1:150835173-150879869	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:42)

SNP	Gene	Cis/trans	Tissue	Source
rs1889741	RP11-316M1.12	cis	Artery Tibial	GTEx
rs1889741	ARNT	cis	parietal	SCAN
rs1889741	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs1889741	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs1889741	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs1889741	PSMD4	cis	parietal	SCAN
rs1889741	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs1889741	HORMAD1	cis	lesional skin	skin_eQTL
rs1889741	ARNT	cis	normal skin	skin_eQTL
rs1889741	HORMAD1	cis	Esophagus Mucosa	GTEx
rs1889741	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs1889741	GNRHR2	cis	cerebellum	SCAN
rs1889741	RP11-316M1.12	cis	lung	GTEx
rs1889741	CTSK	cis	cerebellum	SCAN
rs1889741	RP11-316M1.12	cis	Artery Aorta	GTEx
rs1889741	HORMAD1	cis	Nerve Tibial	GTEx
rs1889741	CTSS	cis	lymphoblastoid	seeQTL
rs1889741	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs1889741	CTSS	cis	cerebellum	SCAN
rs1889741	HORMAD1	cis	parietal	SCAN
rs1889741	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs1889741	HORMAD1	cis	cerebellum	SCAN
rs1889741	CTSS	cis	multi-tissue	Pritchard
rs1889741	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs1889741	CTSS	cis	Thyroid	GTEx
rs1889741	HORMAD1	cis	uninvolved skin	skin_eQTL
rs1889741	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs1889741	RP11-316M1.12	cis	Thyroid	GTEx
rs1889741	HFE2	cis	parietal	SCAN
rs1889741	CTSS	cis	parietal	SCAN
rs1889741	CTSK	cis	parietal	SCAN
rs1889741	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs1889741	RORC	cis	parietal	SCAN
rs1889741	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs1889741	RP11-316M1.12	cis	Whole Blood	GTEx
rs1889741	RP11-98D18.3	cis	Esophagus Mucosa	GTEx
rs1889741	HORMAD1	cis	normal skin	skin_eQTL
rs1889741	ARNT	cis	cerebellum	SCAN
rs1889741	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs1889741	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs1889741	GOLPH3L	cis	Nerve Tibial	GTEx
rs1889741	RP11-316M1.12	cis	Nerve Tibial	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150868600-150874000	Weak transcription	Placenta	Placenta
2	chr1:150869000-150870000	Enhancers	Skeletal Muscle Female	skeletal muscle

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