Variant report

Variant	rs56049576
Chromosome Location	chr1:59015332-59015333
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr1:59014648-59015535	K562	blood:	n/a	n/a
2	NR2F2	chr1:59014743-59015362	K562	blood:	n/a	n/a
3	RAD21	chr1:59015321-59015629	H1-hESC	embryonic stem cell:	n/a	n/a
4	CEBPB	chr1:59014938-59015687	K562	blood:	n/a	n/a
5	MYC	chr1:59015005-59015542	K562	blood:	n/a	n/a
6	JUND	chr1:59014984-59015390	K562	blood:	n/a	n/a
7	CEBPB	chr1:59014986-59015678	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

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

No data

Variant related genes	Relation type
DAB1	TF binding region
OMA1	TF binding region
ENSG00000173406	Chromatin interaction
ENSG00000162600	Chromatin interaction
ENSG00000270209	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10458559	1.00[ASN][1000 genomes]
rs10489815	0.82[ASN][1000 genomes]
rs10789064	1.00[ASN][1000 genomes]
rs10789065	0.97[ASN][1000 genomes]
rs10789066	1.00[ASN][1000 genomes]
rs10889098	0.82[AFR][1000 genomes]
rs10889099	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10889100	1.00[ASN][1000 genomes]
rs10889101	1.00[ASN][1000 genomes]
rs10889104	0.86[EUR][1000 genomes]
rs1109895	1.00[ASN][1000 genomes]
rs1109896	1.00[ASN][1000 genomes]
rs11207238	0.82[ASN][1000 genomes]
rs11207239	0.82[ASN][1000 genomes]
rs11207245	0.81[ASN][1000 genomes]
rs11207246	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207247	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207248	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207250	1.00[ASN][1000 genomes]
rs11207251	1.00[ASN][1000 genomes]
rs11207252	1.00[ASN][1000 genomes]
rs11207253	1.00[ASN][1000 genomes]
rs11207254	1.00[ASN][1000 genomes]
rs11207255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207260	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207262	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207264	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11207265	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11207266	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11207267	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11207268	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11581594	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11582299	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11583248	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11589214	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11589236	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11590757	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11590785	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12058651	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12067296	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12067565	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12068196	0.81[ASN][1000 genomes]
rs12068201	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12068391	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12068457	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12068597	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12069688	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12070503	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12072998	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12077340	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12077766	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12080357	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12087583	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12088905	0.82[ASN][1000 genomes]
rs12092564	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12097882	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12118488	0.82[ASN][1000 genomes]
rs12121129	0.82[ASN][1000 genomes]
rs12125391	1.00[ASN][1000 genomes]
rs12133823	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12139475	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12141238	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12142098	1.00[ASN][1000 genomes]
rs12144759	0.82[ASN][1000 genomes]
rs12406405	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17117742	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17117873	0.86[EUR][1000 genomes]
rs17117877	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2087799	1.00[ASN][1000 genomes]
rs232841	0.84[ASN][1000 genomes]
rs232842	0.84[ASN][1000 genomes]
rs232844	0.84[ASN][1000 genomes]
rs232847	0.84[ASN][1000 genomes]
rs232848	0.88[ASN][1000 genomes]
rs232849	0.88[ASN][1000 genomes]
rs2406784	1.00[ASN][1000 genomes]
rs3087585	0.94[ASN][1000 genomes]
rs34023272	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34135541	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3893156	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3893157	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41313363	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56087605	0.82[ASN][1000 genomes]
rs56138615	0.82[ASN][1000 genomes]
rs562166	0.88[ASN][1000 genomes]
rs584579	0.88[ASN][1000 genomes]
rs59607787	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59924197	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs602579	0.88[ASN][1000 genomes]
rs603031	0.88[ASN][1000 genomes]
rs60490291	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60726128	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61779295	0.84[ASN][1000 genomes]
rs61779296	0.84[ASN][1000 genomes]
rs620342	0.88[ASN][1000 genomes]
rs627218	0.88[ASN][1000 genomes]
rs6587820	0.94[ASN][1000 genomes]
rs6587821	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6663327	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6666138	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6666304	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6679808	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6690139	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6704300	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67264345	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67443104	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67673245	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67805407	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68192782	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72672216	0.94[ASN][1000 genomes]
rs7355165	0.94[ASN][1000 genomes]
rs7355166	0.94[ASN][1000 genomes]
rs7515056	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7536867	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7546900	1.00[ASN][1000 genomes]
rs7547070	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs905567	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
rs56049576	TACSTD2	cis	Whole Blood	GTEx
rs56049576	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59012400-59015400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:59012600-59016200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:59012800-59016000	Enhancers	HepG2	liver
4	chr1:59012800-59016600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:59012800-59017400	Weak transcription	Pancreas	Pancrea
6	chr1:59012800-59017600	Weak transcription	Aorta	Aorta
7	chr1:59013000-59016600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:59013000-59016600	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:59013000-59016600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:59013200-59017000	Weak transcription	Fetal Brain Male	brain
11	chr1:59014200-59015800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr1:59014400-59015800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:59014600-59016400	Enhancers	Fetal Intestine Small	intestine
14	chr1:59014600-59018000	Enhancers	Fetal Lung	lung
15	chr1:59014800-59016000	Enhancers	Primary hematopoietic stem cells	blood
16	chr1:59014800-59017400	Weak transcription	Ovary	ovary
17	chr1:59015200-59015600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr1:59015200-59015800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:59015200-59015800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:59015200-59015800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:59015200-59015800	Flanking Active TSS	K562	blood
22	chr1:59015200-59016200	Enhancers	Fetal Intestine Large	intestine
23	chr1:59015200-59016400	Enhancers	Fetal Kidney	kidney

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