Variant report

Variant	rs11207262
Chromosome Location	chr1:59037867-59037868
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59036779..59041086-chr1:59041779..59044109,4	K562	blood:
2	chr1:59010051..59014308-chr1:59037308..59040619,7	MCF-7	breast:
3	chr1:59016754..59019078-chr1:59037193..59040025,2	MCF-7	breast:
4	chr1:59011375..59015452-chr1:59036952..59041044,5	MCF-7	breast:
5	chr1:58999141..59000957-chr1:59036910..59038987,2	MCF-7	breast:
6	chr1:59015745..59017645-chr1:59037039..59039268,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173406	Chromatin interaction
ENSG00000184292	Chromatin interaction
ENSG00000270209	Chromatin interaction
ENSG00000162600	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10458559	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10489815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs10789064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10789065	0.85[ASN][1000 genomes]
rs10789066	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10889098	0.87[CEU][hapmap];0.95[YRI][hapmap]
rs10889099	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10889100	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10889101	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10889104	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1109895	0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1109896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11207246	0.82[ASN][1000 genomes]
rs11207247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11207248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11207250	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs11207251	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11207252	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11207253	0.88[ASN][1000 genomes]
rs11207254	0.88[ASN][1000 genomes]
rs11207255	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207260	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207264	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207265	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207266	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207267	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207268	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11581594	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11582299	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11583248	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11584788	0.81[EUR][1000 genomes]
rs11589214	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590785	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12030713	1.00[CHB][hapmap]
rs12058651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12067296	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12067565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12068201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12068391	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068597	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12069688	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12070503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[ASN][1000 genomes]
rs12072998	0.82[ASN][1000 genomes]
rs12077340	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12077766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12080357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12087583	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12092564	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12097882	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12125391	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12133823	0.82[ASN][1000 genomes]
rs12139475	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12141238	0.82[ASN][1000 genomes]
rs12142098	0.88[ASN][1000 genomes]
rs12144759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs12406405	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12568356	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17117742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17117873	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs17117877	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17372425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs17461345	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1775002	0.86[CHB][hapmap]
rs2087799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[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	1.00[ASN][1000 genomes]
rs232849	1.00[ASN][1000 genomes]
rs2406784	0.88[ASN][1000 genomes]
rs3087585	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs34023272	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34135541	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3893157	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41313363	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56049576	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs562166	1.00[ASN][1000 genomes]
rs584579	1.00[ASN][1000 genomes]
rs59607787	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59924197	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs602579	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs603031	1.00[ASN][1000 genomes]
rs60490291	0.82[ASN][1000 genomes]
rs60726128	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61779295	0.97[ASN][1000 genomes]
rs61779296	0.97[ASN][1000 genomes]
rs620342	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs627218	1.00[ASN][1000 genomes]
rs6587820	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6587821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs6663327	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6664314	0.81[EUR][1000 genomes]
rs6666138	1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6666304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6679808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6690139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6704300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67238056	0.81[EUR][1000 genomes]
rs67264345	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67443104	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67538366	0.81[EUR][1000 genomes]
rs67673245	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67805407	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68192782	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72672216	0.82[ASN][1000 genomes]
rs7355165	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7355166	0.82[ASN][1000 genomes]
rs7515056	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7536867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[ASN][1000 genomes]
rs7546900	0.88[ASN][1000 genomes]
rs7547070	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs905567	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[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
rs11207262	TACSTD2	cis	Whole Blood	GTEx
rs11207262	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59033800-59039800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:59034400-59039400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:59034600-59039000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:59034600-59039800	Enhancers	Stomach Mucosa	stomach
5	chr1:59034800-59038400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:59035000-59038200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:59035000-59038600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:59035000-59039800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:59035800-59038400	Enhancers	HMEC	breast
10	chr1:59035800-59041000	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr1:59036000-59038000	Enhancers	Brain Substantia Nigra	brain
12	chr1:59036200-59038600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:59036800-59038400	Weak transcription	HSMMtube	muscle
14	chr1:59037000-59039800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:59037400-59038000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr1:59037400-59038200	Enhancers	NHEK	skin
17	chr1:59037400-59038600	Enhancers	GM12878-XiMat	blood
18	chr1:59037600-59038200	Enhancers	Fetal Lung	lung
19	chr1:59037600-59038200	Weak transcription	Pancreas	Pancrea
20	chr1:59037600-59039600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:59037800-59038600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:59037800-59039600	Weak transcription	Esophagus	oesophagus

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