Variant report

Variant	rs232847
Chromosome Location	chr1:59038549-59038550
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:59036779..59041086-chr1:59041779..59044109,4	K562	blood:
2	chr1:59019484..59022044-chr1:59038523..59040233,2	MCF-7	breast:
3	chr1:59034065..59036590-chr1:59038071..59040103,2	K562	blood:
4	chr1:59010051..59014308-chr1:59037308..59040619,7	MCF-7	breast:
5	chr1:59016754..59019078-chr1:59037193..59040025,2	MCF-7	breast:
6	chr1:59011375..59015452-chr1:59036952..59041044,5	MCF-7	breast:
7	chr1:59038080..59040055-chr1:59041779..59043442,2	K562	blood:
8	chr1:58999141..59000957-chr1:59036910..59038987,2	MCF-7	breast:
9	chr1:59015745..59017645-chr1:59037039..59039268,2	MCF-7	breast:
10	chr1:59032420..59036590-chr1:59038071..59040162,4	K562	blood:

No data

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

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10458559	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10789064	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10789065	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10789066	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10789067	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10889100	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10889101	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10889104	0.90[ASN][1000 genomes]
rs1109895	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1109896	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11207250	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11207251	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11207252	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11207253	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11207254	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11207255	0.84[ASN][1000 genomes]
rs11207260	0.97[ASN][1000 genomes]
rs11207262	0.97[ASN][1000 genomes]
rs11207264	0.97[ASN][1000 genomes]
rs11207265	0.97[ASN][1000 genomes]
rs11207266	0.97[ASN][1000 genomes]
rs11207267	0.97[ASN][1000 genomes]
rs11207268	0.97[ASN][1000 genomes]
rs11581594	0.97[ASN][1000 genomes]
rs11582299	0.97[ASN][1000 genomes]
rs11583248	0.97[ASN][1000 genomes]
rs11584788	0.80[ASN][1000 genomes]
rs11589214	0.97[ASN][1000 genomes]
rs11589236	0.97[ASN][1000 genomes]
rs11590757	0.97[ASN][1000 genomes]
rs12030713	0.82[EUR][1000 genomes]
rs12067296	0.97[ASN][1000 genomes]
rs12067565	0.97[ASN][1000 genomes]
rs12068196	0.97[ASN][1000 genomes]
rs12068201	0.97[ASN][1000 genomes]
rs12068391	0.97[ASN][1000 genomes]
rs12068457	0.97[ASN][1000 genomes]
rs12068597	0.97[ASN][1000 genomes]
rs12069688	0.97[ASN][1000 genomes]
rs12077340	0.97[ASN][1000 genomes]
rs12087583	1.00[ASN][1000 genomes]
rs12092564	0.97[ASN][1000 genomes]
rs12097882	0.97[ASN][1000 genomes]
rs12125391	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12142098	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12406405	1.00[ASN][1000 genomes]
rs12568356	0.93[ASN][1000 genomes]
rs17117742	0.84[ASN][1000 genomes]
rs17117877	0.97[ASN][1000 genomes]
rs17461345	0.80[ASN][1000 genomes]
rs1775002	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2087799	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs232822	0.95[EUR][1000 genomes]
rs232826	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs232841	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232842	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232848	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232849	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2406784	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34023272	0.97[ASN][1000 genomes]
rs34135541	0.97[ASN][1000 genomes]
rs3893156	0.97[ASN][1000 genomes]
rs3893157	0.97[ASN][1000 genomes]
rs41313363	1.00[ASN][1000 genomes]
rs486463	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56049576	0.84[ASN][1000 genomes]
rs562166	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs584579	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59607787	0.97[ASN][1000 genomes]
rs59924197	1.00[ASN][1000 genomes]
rs602579	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs603031	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60726128	0.84[ASN][1000 genomes]
rs61779295	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61779296	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620342	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs627218	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6587828	0.83[EUR][1000 genomes]
rs659061	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6663327	0.97[ASN][1000 genomes]
rs6664314	0.80[ASN][1000 genomes]
rs6666138	0.97[ASN][1000 genomes]
rs6666304	0.97[ASN][1000 genomes]
rs6690139	0.97[ASN][1000 genomes]
rs6704300	0.97[ASN][1000 genomes]
rs672359	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67238056	0.80[ASN][1000 genomes]
rs67264345	0.97[ASN][1000 genomes]
rs67443104	0.97[ASN][1000 genomes]
rs67538366	0.80[ASN][1000 genomes]
rs67639631	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs67673245	0.97[ASN][1000 genomes]
rs67805407	0.97[ASN][1000 genomes]
rs68192782	0.97[ASN][1000 genomes]
rs7355165	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7355166	0.86[EUR][1000 genomes]
rs7517424	0.81[EUR][1000 genomes]
rs7520008	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7546900	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7547036	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7547070	1.00[ASN][1000 genomes]
rs905567	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[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
rs232847	TACSTD2	cis	Whole Blood	GTEx
rs232847	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL
rs232847	TACSTD2	cis	Thyroid	GTEx

Chromatin state (count:29 , 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	chr1:59035000-59038600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:59035000-59039800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:59035800-59041000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr1:59036200-59038600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:59037000-59039800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:59037400-59038600	Enhancers	GM12878-XiMat	blood
11	chr1:59037600-59039600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:59037800-59038600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:59037800-59039600	Weak transcription	Esophagus	oesophagus
14	chr1:59038000-59040200	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr1:59038000-59041200	Weak transcription	Brain Substantia Nigra	brain
16	chr1:59038200-59038800	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr1:59038200-59038800	Bivalent Enhancer	Fetal Intestine Large	intestine
18	chr1:59038200-59038800	Weak transcription	Fetal Lung	lung
19	chr1:59038200-59038800	Enhancers	Pancreas	Pancrea
20	chr1:59038200-59039600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr1:59038200-59040200	Flanking Active TSS	NHEK	skin
22	chr1:59038400-59038600	Enhancers	HSMMtube	muscle
23	chr1:59038400-59038800	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr1:59038400-59039000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:59038400-59039000	Flanking Active TSS	HMEC	breast
26	chr1:59038400-59039800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:59038400-59039800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:59038400-59039800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
29	chr1:59038400-59043600	Active TSS	Breast Myoepithelial Primary Cells	Breast

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