Variant report

Variant	rs17461345
Chromosome Location	chr1:59056605-59056606
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59041326..59044486-chr1:59056548..59059729,7	MCF-7	breast:
2	chr1:59039068..59041052-chr1:59055428..59057682,2	MCF-7	breast:
3	chr1:59049910..59054215-chr1:59054903..59060265,8	MCF-7	breast:
4	chr1:59055381..59057219-chr1:59060297..59061966,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184292	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10458559	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10489815	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10789064	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10789066	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10889100	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10889101	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10889104	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1109895	1.00[JPT][hapmap]
rs1109896	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11207247	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11207248	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11207250	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11207251	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11207252	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11207260	0.81[EUR][1000 genomes]
rs11207262	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11207264	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11207265	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11207266	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11207267	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11207268	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11581594	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11582299	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11583248	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11584788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589214	0.81[EUR][1000 genomes]
rs11589236	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11590757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12030713	1.00[CHB][hapmap]
rs12058651	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12067296	0.81[EUR][1000 genomes]
rs12067565	1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs12068196	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12068201	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12068391	0.81[EUR][1000 genomes]
rs12068457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12068597	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12069688	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12070503	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12077340	0.81[EUR][1000 genomes]
rs12077766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs12080357	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs12087583	0.80[ASN][1000 genomes]
rs12092564	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12097882	0.81[EUR][1000 genomes]
rs12118488	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12125391	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12139475	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12144759	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12406405	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12568356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17117742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs17117873	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17117877	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17372425	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1775002	0.82[CHB][hapmap]
rs2087799	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs232841	0.80[ASN][1000 genomes]
rs232842	0.80[ASN][1000 genomes]
rs232844	0.80[ASN][1000 genomes]
rs232847	0.80[ASN][1000 genomes]
rs3087585	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34023272	0.81[EUR][1000 genomes]
rs34135541	0.81[EUR][1000 genomes]
rs3893156	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3893157	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41313363	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59607787	0.81[EUR][1000 genomes]
rs59924197	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs602579	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs61779295	0.80[ASN][1000 genomes]
rs61779296	0.80[ASN][1000 genomes]
rs620342	1.00[CHB][hapmap]
rs6587820	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6587821	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6663327	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6664314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666138	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6666304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6679808	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs6690139	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6704300	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67238056	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67264345	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67443104	0.81[EUR][1000 genomes]
rs67538366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67673245	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67805407	0.81[EUR][1000 genomes]
rs68192782	0.81[EUR][1000 genomes]
rs7355165	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7515056	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7536867	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7547070	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs905567	1.00[CHB][hapmap];1.00[JPT][hapmap]

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
rs17461345	TACSTD2	cis	Whole Blood	GTEx
rs17461345	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59049400-59057800	Weak transcription	Gastric	stomach
2	chr1:59050600-59057400	Weak transcription	Right Atrium	heart
3	chr1:59051200-59063400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr1:59051800-59057600	Weak transcription	A549	lung
5	chr1:59052000-59057200	Weak transcription	Hela-S3	cervix
6	chr1:59052200-59057000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:59052400-59056800	Weak transcription	Aorta	Aorta
8	chr1:59052400-59058000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:59052600-59057800	Weak transcription	NH-A	brain
10	chr1:59052600-59057800	Weak transcription	NHLF	lung
11	chr1:59052800-59057200	Weak transcription	HSMMtube	muscle
12	chr1:59052800-59057400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:59052800-59057400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:59052800-59057400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:59052800-59057400	Weak transcription	Esophagus	oesophagus
16	chr1:59052800-59057400	Weak transcription	Ovary	ovary
17	chr1:59052800-59057400	Weak transcription	HSMM	muscle
18	chr1:59052800-59057600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:59053000-59057200	Weak transcription	HUVEC	blood vessel
20	chr1:59053000-59057600	Weak transcription	Osteobl	bone
21	chr1:59054400-59059400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr1:59054800-59057600	Weak transcription	Placenta	Placenta
23	chr1:59054800-59057800	Weak transcription	Spleen	Spleen
24	chr1:59055000-59060000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:59055200-59056800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:59055200-59058200	Weak transcription	Fetal Lung	lung
27	chr1:59055400-59057000	Weak transcription	NHEK	skin
28	chr1:59056000-59057200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:59056000-59057200	Weak transcription	NHDF-Ad	bronchial
30	chr1:59056000-59059400	Enhancers	Pancreas	Pancrea
31	chr1:59056200-59057400	Weak transcription	Lung	lung
32	chr1:59056200-59057800	Weak transcription	Psoas Muscle	Psoas
33	chr1:59056400-59056800	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:59056400-59058000	Weak transcription	Fetal Stomach	stomach
35	chr1:59056400-59058200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:59056400-59059400	Enhancers	HMEC	breast
37	chr1:59056600-59057200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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