Variant report

Variant	rs61779296
Chromosome Location	chr1:59043457-59043458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:59041245-59043707	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:59043304-59043499	ProgFib	skin:	n/a	n/a
3	HA-E2F1	chr1:59042103-59043524	MCF-7	breast:	n/a	n/a
4	POLR2A	chr1:59041066-59043917	HUVEC	blood vessel:	n/a	n/a
5	ELF1	chr1:59042764-59043458	MCF-7	breast:	n/a	n/a
6	TCF12	chr1:59042553-59043610	MCF-7	breast:	n/a	n/a
7	POLR2A	chr1:59041690-59043463	MCF-7	breast:	n/a	n/a
8	POLR2A	chr1:59042302-59043779	H1-hESC	embryonic stem cell:	n/a	n/a
9	NFIC	chr1:59043370-59044356	GM12878	blood:	n/a	chr1:59043523-59043540
10	GATA3	chr1:59042592-59043587	MCF-7	breast:	n/a	n/a
11	E2F6	chr1:59042001-59043506	H1-hESC	embryonic stem cell:	n/a	n/a
12	EBF1	chr1:59043389-59044236	GM12878	blood:	n/a	n/a
13	SIN3AK20	chr1:59041150-59043543	MCF-7	breast:	n/a	n/a
14	MAX	chr1:59042469-59043482	ECC-1	luminal epithelium:	n/a	n/a
15	PML	chr1:59043423-59044329	GM12878	blood:	n/a	chr1:59043981-59043990
16	EP300	chr1:59042556-59043457	ECC-1	luminal epithelium:	n/a	chr1:59043327-59043340 chr1:59043061-59043070
17	NFIC	chr1:59042748-59043835	ECC-1	luminal epithelium:	n/a	chr1:59043523-59043540
18	RUNX3	chr1:59043225-59044476	GM12878	blood:	n/a	n/a
19	MTA3	chr1:59043117-59044209	GM12878	blood:	n/a	n/a
20	MTA3	chr1:59043016-59044322	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:59038144-59044280	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:59009849..59013755-chr1:59040870..59045611,9	MCF-7	breast:
2	chr1:59038818..59041081-chr1:59043453..59045206,2	K562	blood:
3	chr1:59010302..59014215-chr1:59041338..59045361,8	MCF-7	breast:
4	chr1:59042150..59043809-chr1:59165578..59167965,2	MCF-7	breast:

Variant related genes	Relation type
TACSTD2	TF binding region
ENSG00000173406	Chromatin interaction
ENSG00000162600	Chromatin interaction
ENSG00000162601	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	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232842	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232844	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232847	0.89[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	1.00[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	0.82[EUR][1000 genomes]
rs67673245	0.97[ASN][1000 genomes]
rs67805407	0.97[ASN][1000 genomes]
rs68192782	0.97[ASN][1000 genomes]
rs7355165	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7355166	0.86[EUR][1000 genomes]
rs7517424	0.81[EUR][1000 genomes]
rs7520008	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
rs61779296	TACSTD2	cis	Thyroid	GTEx
rs61779296	TACSTD2	cis	Whole Blood	GTEx
rs61779296	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59038400-59043600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr1:59040200-59043600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:59041200-59044200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
4	chr1:59041400-59043800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr1:59041400-59043800	Bivalent Enhancer	Fetal Heart	heart
6	chr1:59041600-59043600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:59041800-59043600	Bivalent Enhancer	Fetal Brain Male	brain
8	chr1:59042000-59043800	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:59042200-59043600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr1:59042200-59043600	Active TSS	Rectal Smooth Muscle	rectum
11	chr1:59042400-59043600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr1:59042400-59043600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
13	chr1:59042600-59043600	Active TSS	Esophagus	oesophagus
14	chr1:59042600-59044200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
15	chr1:59042800-59043600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:59042800-59044000	Enhancers	Brain Angular Gyrus	brain
17	chr1:59043000-59043600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
18	chr1:59043000-59043600	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:59043000-59043600	Bivalent/Poised TSS	Colonic Mucosa	Colon
20	chr1:59043000-59043800	Bivalent Enhancer	NHLF	lung
21	chr1:59043000-59044000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr1:59043200-59043600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:59043200-59043600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
24	chr1:59043200-59043600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:59043200-59043600	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr1:59043200-59043600	Bivalent Enhancer	Liver	Liver
27	chr1:59043200-59043600	Enhancers	Brain Substantia Nigra	brain
28	chr1:59043200-59043600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
29	chr1:59043200-59043600	Bivalent Enhancer	Fetal Muscle Leg	muscle
30	chr1:59043200-59043600	Bivalent Enhancer	Osteobl	bone
31	chr1:59043200-59043800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:59043200-59044000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:59043200-59044000	Bivalent Enhancer	Brain Germinal Matrix	brain
34	chr1:59043200-59044000	Flanking Bivalent TSS/Enh	NHDF-Ad	bronchial
35	chr1:59043200-59044200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
36	chr1:59043200-59044200	Enhancers	Brain Anterior Caudate	brain
37	chr1:59043200-59044200	Flanking Active TSS	GM12878-XiMat	blood
38	chr1:59043200-59044200	Flanking Active TSS	Hela-S3	cervix
39	chr1:59043200-59044200	Flanking Active TSS	HMEC	breast
40	chr1:59043200-59047400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:59043200-59049200	Weak transcription	Gastric	stomach
42	chr1:59043400-59043600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:59043400-59043600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
44	chr1:59043400-59043600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
45	chr1:59043400-59043600	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr1:59043400-59043600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
47	chr1:59043400-59043600	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr1:59043400-59043600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
49	chr1:59043400-59043600	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
50	chr1:59043400-59043600	Bivalent Enhancer	Fetal Stomach	stomach

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