Variant report

Variant	rs12493289
Chromosome Location	chr3:48905161-48905162
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	chr3:48884691..48886196-chr3:48903180..48905510,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224424	Chromatin interaction
ENSG00000114302	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10780033	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130176	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1134591	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11705737	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11705888	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11706052	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11706983	1.00[JPT][hapmap]
rs11708022	0.84[ASN][1000 genomes]
rs11708786	1.00[JPT][hapmap]
rs11709246	0.95[ASN][1000 genomes]
rs11712982	0.82[ASN][1000 genomes]
rs11713694	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11717978	0.85[ASN][1000 genomes]
rs11719291	1.00[JPT][hapmap]
rs11719457	0.85[ASN][1000 genomes]
rs11920534	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11924597	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11928552	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs12491743	0.80[EUR][1000 genomes]
rs12493578	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs12497850	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs12637037	0.86[EUR][1000 genomes]
rs13064883	0.93[EUR][1000 genomes]
rs13064911	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13072911	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13073997	0.90[ASN][1000 genomes]
rs13076394	0.94[EUR][1000 genomes]
rs13078308	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13086240	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13087930	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13090839	0.82[ASN][1000 genomes]
rs13092715	1.00[JPT][hapmap]
rs13094900	0.87[ASN][1000 genomes]
rs13315711	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13316620	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs13434258	1.00[JPT][hapmap]
rs1352420	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs17080319	1.00[JPT][hapmap]
rs28642807	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34037363	1.00[JPT][hapmap]
rs34477108	0.85[ASN][1000 genomes]
rs34509487	0.85[ASN][1000 genomes]
rs35064573	1.00[JPT][hapmap]
rs3774628	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4072859	0.90[EUR][1000 genomes]
rs4858798	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs4858828	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs4858831	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs4974078	0.83[ASN][1000 genomes]
rs4974079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4974080	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4974082	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4974084	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4974085	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974091	0.87[EUR][1000 genomes]
rs56318350	0.85[ASN][1000 genomes]
rs6414613	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6442130	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6446196	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6446198	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6446205	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6446252	1.00[CEU][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6446253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67060340	0.90[ASN][1000 genomes]
rs67332931	0.95[ASN][1000 genomes]
rs6768433	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6772452	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6781790	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6786665	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6788650	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs6789285	0.88[EUR][1000 genomes]
rs6791234	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6791542	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6795025	0.86[EUR][1000 genomes]
rs6796790	0.82[YRI][hapmap]
rs6801211	0.83[YRI][hapmap]
rs71324924	0.95[ASN][1000 genomes]
rs7372149	0.86[EUR][1000 genomes]
rs7373778	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7373790	0.85[EUR][1000 genomes]
rs7430198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7430501	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7431710	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7431857	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7432989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs7612459	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7615235	0.83[EUR][1000 genomes]
rs7615675	0.90[EUR][1000 genomes]
rs7616815	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7621015	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs7623023	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7626445	0.83[EUR][1000 genomes]
rs7627404	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7628719	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7630742	0.83[EUR][1000 genomes]
rs7636057	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7639332	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7643368	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7647093	0.88[EUR][1000 genomes]
rs7647813	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7649458	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7653459	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8926	0.87[EUR][1000 genomes]
rs9284885	0.82[YRI][hapmap]
rs9311430	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9311432	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9311433	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9311434	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9637481	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs9681717	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9682444	1.00[CEU][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9754878	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9755490	1.00[CEU][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9811027	1.00[JPT][hapmap]
rs9830636	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9834996	1.00[JPT][hapmap]
rs9835307	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9840684	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9846123	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9850134	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9867373	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9873726	1.00[JPT][hapmap]
rs9876848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9879971	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9882549	1.00[JPT][hapmap]
rs9884022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487342	chr3:48823957-48960475	Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	esv3487343	chr3:48823963-48960381	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs12493289	AMT	cis	Thyroid	GTEx
rs12493289	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs12493289	NCKIPSD	cis	Whole Blood	GTEx
rs12493289	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs12493289	ARIH2	cis	Thyroid	GTEx
rs12493289	WDR6	cis	Nerve Tibial	GTEx
rs12493289	AMT	cis	Whole Blood	GTEx
rs12493289	WDR6	cis	Heart Left Ventricle	GTEx
rs12493289	WDR6	cis	uninvolved skin	skin_eQTL
rs12493289	WDR6	cis	lung	GTEx
rs12493289	AMT	cis	Artery Aorta	GTEx
rs12493289	WDR6	cis	Whole Blood	GTEx
rs12493289	AMT	cis	Muscle Skeletal	GTEx
rs12493289	NCKIPSD	cis	Muscle Skeletal	GTEx
rs12493289	NCKIPSD	cis	Nerve Tibial	GTEx
rs12493289	NICN1-AS1	cis	Thyroid	GTEx
rs12493289	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs12493289	WDR6	cis	Adipose Subcutaneous	GTEx
rs12493289	WDR6	cis	Artery Tibial	GTEx
rs12493289	NICN1	cis	Thyroid	GTEx
rs12493289	WDR6	cis	Esophagus Muscularis	GTEx
rs12493289	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs12493289	CCDC36	cis	Artery Tibial	GTEx
rs12493289	WDR6	cis	Muscle Skeletal	GTEx
rs12493289	WDR6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48885600-48915000	Weak transcription	Small Intestine	intestine
2	chr3:48885800-48906600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:48885800-48913600	Weak transcription	Fetal Lung	lung
4	chr3:48889600-48935400	Weak transcription	Brain Germinal Matrix	brain
5	chr3:48889800-48916800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:48894400-48923000	Strong transcription	Fetal Intestine Small	intestine
7	chr3:48894600-48918800	Weak transcription	HepG2	liver
8	chr3:48896400-48934400	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:48896600-48918600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:48896800-48934200	Weak transcription	Stomach Mucosa	stomach
11	chr3:48896800-48935000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:48897000-48911800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr3:48897000-48916600	Weak transcription	GM12878-XiMat	blood
14	chr3:48897000-48918400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:48897000-48918800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:48897000-48921400	Weak transcription	Primary B cells from cord blood	blood
17	chr3:48897000-48928600	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:48897000-48933600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:48897000-48934200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:48897000-48934200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:48897200-48907000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:48897200-48916600	Weak transcription	Aorta	Aorta
23	chr3:48897200-48918400	Weak transcription	Gastric	stomach
24	chr3:48897200-48918800	Weak transcription	Ovary	ovary
25	chr3:48897200-48918800	Weak transcription	Psoas Muscle	Psoas
26	chr3:48897200-48923200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:48897200-48924400	Weak transcription	HSMMtube	muscle
28	chr3:48897200-48934200	Weak transcription	Colonic Mucosa	Colon
29	chr3:48897200-48935000	Weak transcription	NH-A	brain
30	chr3:48897200-48935200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:48897400-48918800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:48897400-48921400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr3:48897400-48934600	Weak transcription	Brain Anterior Caudate	brain
34	chr3:48898600-48916800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr3:48900000-48906600	Weak transcription	Left Ventricle	heart
36	chr3:48900000-48909400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:48900000-48909600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:48900000-48915200	Weak transcription	Fetal Stomach	stomach
39	chr3:48900000-48916600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:48900000-48918200	Weak transcription	Right Ventricle	heart
41	chr3:48900000-48922400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr3:48900200-48906000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:48900200-48906400	Weak transcription	Adipose Nuclei	Adipose
44	chr3:48900200-48906400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:48900200-48907000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:48900200-48907600	Weak transcription	Fetal Thymus	thymus
47	chr3:48900200-48909600	Weak transcription	Thymus	Thymus
48	chr3:48900200-48913000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:48900200-48913000	Weak transcription	Spleen	Spleen
50	chr3:48900200-48914200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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