Variant report

Variant	rs10458559
Chromosome Location	chr1:59016250-59016251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59015745..59017645-chr1:59037039..59039268,2	MCF-7	breast:
2	chr1:59014802..59017431-chr1:59018623..59020469,2	K562	blood:
3	chr1:59010376..59013266-chr1:59015138..59019159,5	K562	blood:
4	chr1:58981796..58983981-chr1:59013881..59016702,2	K562	blood:
5	chr1:59010739..59013825-chr1:59014370..59019048,5	K562	blood:
6	chr1:59013352..59015102-chr1:59015166..59016765,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162600	Chromatin interaction
ENSG00000270209	Chromatin interaction
ENSG00000173406	Chromatin interaction

Extended variants
information (count: 139 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs10489815	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10789063	0.80[EUR][1000 genomes]
rs10789064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789065	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10789066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789067	0.91[CEU][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10889099	0.94[ASN][1000 genomes]
rs10889100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889101	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1109895	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1109896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207238	0.82[ASN][1000 genomes]
rs11207239	0.82[ASN][1000 genomes]
rs11207245	0.81[ASN][1000 genomes]
rs11207246	0.94[ASN][1000 genomes]
rs11207247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11207248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11207250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207253	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207254	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207255	1.00[ASN][1000 genomes]
rs11207260	0.88[ASN][1000 genomes]
rs11207262	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11207264	0.81[ASN][1000 genomes]
rs11207265	0.81[ASN][1000 genomes]
rs11207266	0.81[ASN][1000 genomes]
rs11207267	0.81[ASN][1000 genomes]
rs11207268	0.81[ASN][1000 genomes]
rs11581395	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs11581594	0.81[ASN][1000 genomes]
rs11582299	0.81[ASN][1000 genomes]
rs11583248	0.81[ASN][1000 genomes]
rs11589214	0.88[ASN][1000 genomes]
rs11589236	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11590757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11590785	0.94[ASN][1000 genomes]
rs12030713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12058651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12067296	0.88[ASN][1000 genomes]
rs12067565	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs12068196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12068201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12068391	0.88[ASN][1000 genomes]
rs12068457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12068597	0.81[ASN][1000 genomes]
rs12069688	0.81[ASN][1000 genomes]
rs12070503	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12072998	0.94[ASN][1000 genomes]
rs12077340	0.88[ASN][1000 genomes]
rs12077766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12080357	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12087583	0.84[ASN][1000 genomes]
rs12088905	0.82[ASN][1000 genomes]
rs12092564	0.81[ASN][1000 genomes]
rs12097882	0.88[ASN][1000 genomes]
rs12118488	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12121129	0.82[ASN][1000 genomes]
rs12124662	0.95[CEU][hapmap]
rs12125391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133823	0.94[ASN][1000 genomes]
rs12139475	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12141238	0.94[ASN][1000 genomes]
rs12142098	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144759	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12406405	0.84[ASN][1000 genomes]
rs17117742	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17117873	1.00[JPT][hapmap]
rs17117877	0.81[ASN][1000 genomes]
rs17372425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17461345	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1775002	0.86[CHB][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2087799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232822	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs232826	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs232841	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs232842	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs232844	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs232847	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs232848	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs232849	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2406784	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34023272	0.88[ASN][1000 genomes]
rs34135541	0.88[ASN][1000 genomes]
rs3893156	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3893157	0.81[ASN][1000 genomes]
rs41313363	0.84[ASN][1000 genomes]
rs486463	0.95[CEU][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4912195	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs56049576	1.00[ASN][1000 genomes]
rs56087605	0.82[ASN][1000 genomes]
rs56138615	0.82[ASN][1000 genomes]
rs562166	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs584579	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59607787	0.88[ASN][1000 genomes]
rs59924197	0.84[ASN][1000 genomes]
rs602579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs603031	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60490291	0.94[ASN][1000 genomes]
rs60726128	1.00[ASN][1000 genomes]
rs61779295	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61779296	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs620342	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs627218	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6587818	0.80[EUR][1000 genomes]
rs6587819	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs6587820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6587821	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6587828	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs659061	0.91[CEU][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6663327	0.81[ASN][1000 genomes]
rs6666138	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6666304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6679808	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6687324	0.95[CEU][hapmap]
rs6690139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6704300	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs672359	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67264345	0.81[ASN][1000 genomes]
rs67443104	0.88[ASN][1000 genomes]
rs67639631	0.93[EUR][1000 genomes]
rs67673245	0.81[ASN][1000 genomes]
rs67805407	0.88[ASN][1000 genomes]
rs68192782	0.88[ASN][1000 genomes]
rs72672216	0.94[ASN][1000 genomes]
rs7355165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7355166	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7515056	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7517424	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7520008	0.93[EUR][1000 genomes]
rs7536230	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs7536867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7546900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547036	0.95[CEU][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7547070	0.84[ASN][1000 genomes]
rs905567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs10458559	TACSTD2	cis	Thyroid	GTEx
rs10458559	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59012800-59016600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:59012800-59017400	Weak transcription	Pancreas	Pancrea
3	chr1:59012800-59017600	Weak transcription	Aorta	Aorta
4	chr1:59013000-59016600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:59013000-59016600	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:59013000-59016600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:59013200-59017000	Weak transcription	Fetal Brain Male	brain
8	chr1:59014600-59016400	Enhancers	Fetal Intestine Small	intestine
9	chr1:59014600-59018000	Enhancers	Fetal Lung	lung
10	chr1:59014800-59017400	Weak transcription	Ovary	ovary
11	chr1:59015200-59016400	Enhancers	Fetal Kidney	kidney
12	chr1:59015800-59016800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:59015800-59017800	Enhancers	K562	blood
14	chr1:59016000-59016400	Weak transcription	Placenta	Placenta
15	chr1:59016200-59016400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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