Variant report

Variant	rs11589458
Chromosome Location	chr1:150792616-150792617
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:150549484..150553989-chr1:150792406..150795277,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143384	Chromatin interaction

Extended variants
information (count: 159 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:152)

rs_ID	r²[population]
rs1027699	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10305664	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10305667	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10305672	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10305673	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10305704	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10305711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10305714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10305720	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10399947	0.92[EUR][1000 genomes]
rs10788792	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10788794	0.81[EUR][1000 genomes]
rs10888391	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs10888392	0.84[EUR][1000 genomes]
rs10888393	0.90[EUR][1000 genomes]
rs10888394	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs10888395	0.86[EUR][1000 genomes]
rs10888397	0.84[YRI][hapmap];0.91[EUR][1000 genomes]
rs10888398	0.84[EUR][1000 genomes]
rs11204691	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11204697	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11204698	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11204704	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11204722	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs11204723	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11204726	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs11204733	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204739	0.93[EUR][1000 genomes]
rs11204742	0.90[EUR][1000 genomes]
rs11204743	0.81[EUR][1000 genomes]
rs11204750	0.84[EUR][1000 genomes]
rs1136808	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs11552229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11581757	0.84[YRI][hapmap];0.91[EUR][1000 genomes]
rs11582281	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11586422	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11587444	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11589886	0.80[EUR][1000 genomes]
rs11800855	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11803569	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11803940	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11804276	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11807409	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11807450	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs12059949	0.84[EUR][1000 genomes]
rs12063547	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12068264	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12072339	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12075597	0.80[EUR][1000 genomes]
rs12085336	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12086472	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12089989	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12090215	0.91[EUR][1000 genomes]
rs12096831	0.94[EUR][1000 genomes]
rs12097963	0.93[EUR][1000 genomes]
rs12402939	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12403255	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12404949	0.81[EUR][1000 genomes]
rs12406660	0.81[ASN][1000 genomes]
rs12409208	0.94[EUR][1000 genomes]
rs12410394	0.94[EUR][1000 genomes]
rs12410869	0.86[EUR][1000 genomes]
rs1336899	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1336900	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs1415148	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs1532770	0.80[EUR][1000 genomes]
rs1546376	0.84[EUR][1000 genomes]
rs16827671	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs16841797	0.89[YRI][hapmap]
rs17658705	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs17660092	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1889740	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1889741	0.85[EUR][1000 genomes]
rs2089082	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124952	0.85[EUR][1000 genomes]
rs2184833	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2228099	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2230061	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2256355	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2272214	0.85[EUR][1000 genomes]
rs2275235	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2275236	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2280078	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2864869	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2864871	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2864873	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2864882	0.84[EUR][1000 genomes]
rs2867296	0.85[EUR][1000 genomes]
rs2867301	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2867302	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs34985895	0.84[EUR][1000 genomes]
rs36008098	0.86[EUR][1000 genomes]
rs3754212	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3768005	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap]
rs3768013	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768015	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768016	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768018	0.87[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs3843843	0.85[EUR][1000 genomes]
rs4451553	0.81[EUR][1000 genomes]
rs4509581	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4537557	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4970928	0.87[EUR][1000 genomes]
rs4970929	0.86[EUR][1000 genomes]
rs4970930	0.91[EUR][1000 genomes]
rs4970980	0.86[EUR][1000 genomes]
rs4970982	0.94[EUR][1000 genomes]
rs4970984	0.84[EUR][1000 genomes]
rs4970985	0.84[EUR][1000 genomes]
rs4970986	0.86[EUR][1000 genomes]
rs57818453	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59024312	0.86[EUR][1000 genomes]
rs59337856	0.84[EUR][1000 genomes]
rs6587516	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6587518	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs6657388	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6658066	0.82[EUR][1000 genomes]
rs6660084	0.84[EUR][1000 genomes]
rs6660845	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6661415	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6669855	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6671737	0.91[EUR][1000 genomes]
rs6678013	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs66847267	0.84[EUR][1000 genomes]
rs6693120	0.87[EUR][1000 genomes]
rs6700022	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs72704639	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72704652	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72704654	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72704656	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72704658	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72704679	0.82[EUR][1000 genomes]
rs72704682	0.88[EUR][1000 genomes]
rs72704685	0.87[EUR][1000 genomes]
rs7412396	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs7418501	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7511673	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7514004	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7521592	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7521898	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7524620	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7526489	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7528773	0.86[EUR][1000 genomes]
rs7529194	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7532045	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7538493	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7540874	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7556661	0.91[EUR][1000 genomes]
rs8444	0.84[EUR][1000 genomes]
rs868751	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs897815	0.91[EUR][1000 genomes]
rs951281	0.91[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	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
6	nsv2788	chr1:150755334-150800785	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv872420	chr1:150786038-150847647	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs11589458	GOLPH3L	cis	Nerve Tibial	GTEx
rs11589458	CTSS	cis	multi-tissue	Pritchard
rs11589458	CTSS	cis	Thyroid	GTEx
rs11589458	RP11-316M1.12	cis	lung	GTEx
rs11589458	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs11589458	CTSS	cis	Artery Tibial	GTEx
rs11589458	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs11589458	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs11589458	RP11-316M1.12	cis	Artery Aorta	GTEx
rs11589458	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs11589458	RP11-316M1.12	cis	Whole Blood	GTEx
rs11589458	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs11589458	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs11589458	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs11589458	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs11589458	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs11589458	RP11-316M1.12	cis	Thyroid	GTEx
rs11589458	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs11589458	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs11589458	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs11589458	HORMAD1	cis	Esophagus Mucosa	GTEx
rs11589458	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs11589458	RP11-316M1.12	cis	Artery Tibial	GTEx
rs11589458	HORMAD1	cis	Nerve Tibial	GTEx
rs11589458	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150765400-150793600	Weak transcription	Fetal Heart	heart
2	chr1:150782200-150795800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:150782200-150809600	Strong transcription	Fetal Muscle Leg	muscle
4	chr1:150782200-150809800	Strong transcription	Stomach Smooth Muscle	stomach
5	chr1:150782200-150813000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:150782400-150812200	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr1:150782600-150796600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:150782600-150802800	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:150782800-150792800	Strong transcription	Placenta	Placenta
10	chr1:150782800-150795800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:150783000-150795800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:150783000-150797000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:150783200-150794000	Strong transcription	HSMM	muscle
14	chr1:150783200-150795800	Strong transcription	NH-A	brain
15	chr1:150783200-150796000	Strong transcription	Adipose Nuclei	Adipose
16	chr1:150783200-150796000	Strong transcription	Duodenum Mucosa	Duodenum
17	chr1:150783200-150797000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:150783200-150809800	Strong transcription	Fetal Thymus	thymus
19	chr1:150783200-150816600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:150783200-150816800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:150783400-150793400	Strong transcription	Osteobl	bone
22	chr1:150784000-150802000	Strong transcription	Fetal Lung	lung
23	chr1:150784200-150795000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:150784200-150796000	Strong transcription	Fetal Intestine Large	intestine
25	chr1:150785800-150793000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:150785800-150793000	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:150785800-150793200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr1:150785800-150806400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:150785800-150812400	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr1:150786000-150793800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:150786000-150796000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:150786000-150808600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:150786800-150793400	Weak transcription	Fetal Kidney	kidney
34	chr1:150786800-150794800	Weak transcription	Gastric	stomach
35	chr1:150788200-150796000	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr1:150788400-150793200	Strong transcription	NHDF-Ad	bronchial
37	chr1:150788400-150795800	Strong transcription	Primary T cells from cord blood	blood
38	chr1:150788400-150795800	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr1:150788400-150795800	Strong transcription	Brain Substantia Nigra	brain
40	chr1:150788400-150795800	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:150788400-150796000	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:150788400-150808000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr1:150788400-150809800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr1:150788400-150812200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:150788600-150795600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:150788800-150793400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:150788800-150795800	Strong transcription	Ovary	ovary
48	chr1:150788800-150797200	Strong transcription	HUVEC	blood vessel
49	chr1:150789400-150794200	Weak transcription	Psoas Muscle	Psoas
50	chr1:150789400-150794800	Weak transcription	H9 Cell Line	embryonic stem cell

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