Variant report

Variant	rs620342
Chromosome Location	chr1:59034901-59034902
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59027310..59029958-chr1:59032688..59035404,2	MCF-7	breast:
2	chr1:59032420..59036590-chr1:59038071..59040162,4	K562	blood:
3	chr1:59034065..59036590-chr1:59038071..59040103,2	K562	blood:
4	chr1:59033300..59036238-chr1:59156402..59159118,2	MCF-7	breast:

Extended variants
information (count: 135 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs10458559	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]
rs10489815	1.00[CHB][hapmap]
rs10789064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10789065	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10789066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10789067	0.91[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10889099	0.82[ASN][1000 genomes]
rs10889100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10889101	0.84[CEU][hapmap];0.85[CHB][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10889104	0.88[ASN][1000 genomes]
rs1109895	0.95[CEU][hapmap];0.84[CHB][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1109896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207246	0.82[ASN][1000 genomes]
rs11207247	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs11207248	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs11207250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207253	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207254	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207255	0.88[ASN][1000 genomes]
rs11207260	1.00[ASN][1000 genomes]
rs11207262	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11207264	0.94[ASN][1000 genomes]
rs11207265	0.94[ASN][1000 genomes]
rs11207266	0.94[ASN][1000 genomes]
rs11207267	0.94[ASN][1000 genomes]
rs11207268	0.94[ASN][1000 genomes]
rs11581395	0.95[CEU][hapmap]
rs11581594	0.94[ASN][1000 genomes]
rs11582299	0.94[ASN][1000 genomes]
rs11583248	0.94[ASN][1000 genomes]
rs11589214	1.00[ASN][1000 genomes]
rs11589236	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11590757	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11590785	0.82[ASN][1000 genomes]
rs12030713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs12058651	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12067296	1.00[ASN][1000 genomes]
rs12067565	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12068196	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs12068201	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs12068391	1.00[ASN][1000 genomes]
rs12068457	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12068597	0.94[ASN][1000 genomes]
rs12069688	0.94[ASN][1000 genomes]
rs12070503	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12072998	0.82[ASN][1000 genomes]
rs12077340	1.00[ASN][1000 genomes]
rs12077766	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12080357	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12087583	0.97[ASN][1000 genomes]
rs12092564	0.94[ASN][1000 genomes]
rs12097882	1.00[ASN][1000 genomes]
rs12118488	1.00[CHB][hapmap]
rs12124662	0.95[CEU][hapmap]
rs12125391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12133823	0.82[ASN][1000 genomes]
rs12139475	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12141238	0.82[ASN][1000 genomes]
rs12142098	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12144759	1.00[CHB][hapmap]
rs12406405	0.97[ASN][1000 genomes]
rs12568356	0.90[ASN][1000 genomes]
rs17117742	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs17117877	0.94[ASN][1000 genomes]
rs17372425	1.00[CHB][hapmap]
rs17461345	1.00[CHB][hapmap]
rs1775002	0.86[CHB][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2087799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs232822	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs232826	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs232827	0.84[AMR][1000 genomes]
rs232830	0.83[AMR][1000 genomes]
rs232841	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232842	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232844	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232847	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232848	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232849	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406784	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3087585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs34023272	1.00[ASN][1000 genomes]
rs34135541	1.00[ASN][1000 genomes]
rs3551	0.84[AMR][1000 genomes]
rs3893156	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs3893157	0.94[ASN][1000 genomes]
rs41313363	0.97[ASN][1000 genomes]
rs486463	0.95[CEU][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4912195	0.95[CEU][hapmap]
rs525929	0.82[AMR][1000 genomes]
rs56049576	0.88[ASN][1000 genomes]
rs562166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs584579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59607787	1.00[ASN][1000 genomes]
rs59924197	0.97[ASN][1000 genomes]
rs602579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603031	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60490291	0.82[ASN][1000 genomes]
rs60726128	0.88[ASN][1000 genomes]
rs61779295	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61779296	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs627218	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587819	0.91[CEU][hapmap]
rs6587820	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs6587821	1.00[CHB][hapmap]
rs6587828	0.83[EUR][1000 genomes]
rs659061	0.91[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6663327	0.94[ASN][1000 genomes]
rs6666138	0.94[ASN][1000 genomes]
rs6666304	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs6679808	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs6687324	0.95[CEU][hapmap]
rs6690139	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs6704300	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs672359	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67264345	0.94[ASN][1000 genomes]
rs67443104	1.00[ASN][1000 genomes]
rs67639631	0.82[EUR][1000 genomes]
rs67673245	0.94[ASN][1000 genomes]
rs67805407	1.00[ASN][1000 genomes]
rs68192782	1.00[ASN][1000 genomes]
rs72672216	0.82[ASN][1000 genomes]
rs7355165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7355166	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7515056	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs7517424	0.81[EUR][1000 genomes]
rs7520008	0.82[EUR][1000 genomes]
rs7536230	0.95[CEU][hapmap]
rs7536867	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs7546900	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7547036	0.95[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7547070	0.97[ASN][1000 genomes]
rs905567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs620342	TACSTD2	cis	Thyroid	GTEx
rs620342	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL
rs620342	TACSTD2	cis	Whole Blood	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59031600-59035000	Enhancers	Psoas Muscle	Psoas
2	chr1:59032600-59035000	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr1:59033000-59035000	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr1:59033400-59035000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr1:59033400-59035000	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr1:59033800-59035000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:59033800-59035400	Enhancers	NHEK	skin
8	chr1:59033800-59039800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:59034200-59035200	Enhancers	H9 Cell Line	embryonic stem cell
10	chr1:59034200-59036200	Enhancers	GM12878-XiMat	blood
11	chr1:59034400-59035000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:59034400-59035000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr1:59034400-59035000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:59034400-59036000	Weak transcription	Esophagus	oesophagus
15	chr1:59034400-59037400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:59034400-59039400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:59034600-59035000	Enhancers	Duodenum Mucosa	Duodenum
18	chr1:59034600-59039000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:59034600-59039800	Enhancers	Stomach Mucosa	stomach
20	chr1:59034800-59035800	Weak transcription	HMEC	breast
21	chr1:59034800-59038400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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