Variant report

Variant	rs12069688
Chromosome Location	chr1:59051635-59051636
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59047843..59052771-chr1:59082760..59087529,8	MCF-7	breast:
2	chr1:59048457..59052619-chr1:59081708..59087602,8	MCF-7	breast:
3	chr1:59049910..59054215-chr1:59054903..59060265,8	MCF-7	breast:
4	chr1:59049755..59053628-chr1:59060314..59062387,4	MCF-7	breast:

Extended variants
information (count: 111 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10458559	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10489815	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10789064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10789066	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10889099	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10889100	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10889101	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10889104	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1109895	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1109896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11207247	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11207248	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs11207250	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11207251	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11207252	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11207253	0.81[ASN][1000 genomes]
rs11207254	0.81[ASN][1000 genomes]
rs11207255	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11207260	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207262	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207264	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207265	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207266	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207267	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207268	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11581594	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582299	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11583248	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584788	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11589214	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11589236	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11590757	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11590785	0.83[EUR][1000 genomes]
rs12030713	1.00[CHB][hapmap]
rs12058651	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs12067296	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12067565	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12068196	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068201	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068391	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12068457	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12068597	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070503	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12077340	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12077766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12080357	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs12087583	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12092564	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12097882	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12118488	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12125391	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12139475	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12142098	0.81[ASN][1000 genomes]
rs12144759	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12406405	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12568356	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17117742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17117873	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17117877	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17372425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17461345	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1775002	0.82[CHB][hapmap]
rs2087799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs232841	0.97[ASN][1000 genomes]
rs232842	0.97[ASN][1000 genomes]
rs232844	0.97[ASN][1000 genomes]
rs232847	0.97[ASN][1000 genomes]
rs232848	0.94[ASN][1000 genomes]
rs232849	0.94[ASN][1000 genomes]
rs2406784	0.81[ASN][1000 genomes]
rs3087585	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34023272	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34135541	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3893156	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893157	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41313363	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56049576	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs562166	0.94[ASN][1000 genomes]
rs584579	0.94[ASN][1000 genomes]
rs59607787	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59924197	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs602579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs603031	0.94[ASN][1000 genomes]
rs60726128	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61779295	0.97[ASN][1000 genomes]
rs61779296	0.97[ASN][1000 genomes]
rs620342	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs627218	0.94[ASN][1000 genomes]
rs6587820	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6587821	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6663327	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664314	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6666138	1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679808	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs6690139	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704300	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67238056	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67264345	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67443104	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67538366	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67673245	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67805407	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68192782	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7355165	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7515056	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7536867	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7546900	0.81[ASN][1000 genomes]
rs7547070	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs905567	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12069688	TACSTD2	cis	Whole Blood	GTEx
rs12069688	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59049000-59052000	Enhancers	HSMMtube	muscle
2	chr1:59049000-59052200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:59049000-59052400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr1:59049000-59052400	Enhancers	Fetal Lung	lung
5	chr1:59049000-59052800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:59049000-59052800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:59049200-59052400	Enhancers	Aorta	Aorta
8	chr1:59049200-59052400	Enhancers	NHDF-Ad	bronchial
9	chr1:59049200-59052800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:59049200-59052800	Enhancers	Esophagus	oesophagus
11	chr1:59049400-59057800	Weak transcription	Gastric	stomach
12	chr1:59049800-59052800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:59049800-59052800	Enhancers	Ovary	ovary
14	chr1:59050000-59051800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:59050200-59052400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:59050200-59052800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:59050200-59052800	Enhancers	HMEC	breast
18	chr1:59050200-59052800	Enhancers	HSMM	muscle
19	chr1:59050200-59053000	Enhancers	HUVEC	blood vessel
20	chr1:59050400-59052000	Enhancers	Hela-S3	cervix
21	chr1:59050400-59052400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:59050400-59052400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:59050400-59052600	Enhancers	NH-A	brain
24	chr1:59050400-59052600	Enhancers	NHLF	lung
25	chr1:59050400-59052800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:59050600-59051800	Enhancers	A549	lung
27	chr1:59050600-59052800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:59050600-59053000	Enhancers	Osteobl	bone
29	chr1:59050600-59057400	Weak transcription	Right Atrium	heart
30	chr1:59050800-59052200	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr1:59050800-59052600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:59051000-59051800	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr1:59051000-59052000	Enhancers	NHEK	skin
34	chr1:59051200-59052000	Weak transcription	Lung	lung
35	chr1:59051200-59056000	Weak transcription	Pancreas	Pancrea
36	chr1:59051200-59063400	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:59051400-59051800	Weak transcription	Spleen	Spleen
38	chr1:59051600-59051800	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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