Variant report

Variant	rs1775002
Chromosome Location	chr1:59016600-59016601
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:59016487-59016830	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:59015745..59017645-chr1:59037039..59039268,2	MCF-7	breast:
2	chr1:59014802..59017431-chr1:59018623..59020469,2	K562	blood:
3	chr1:59010376..59013266-chr1:59015138..59019159,5	K562	blood:
4	chr1:58981796..58983981-chr1:59013881..59016702,2	K562	blood:
5	chr1:59010739..59013825-chr1:59014370..59019048,5	K562	blood:
6	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
ENSG00000162600	Chromatin interaction
ENSG00000270209	Chromatin interaction
ENSG00000173406	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10458559	0.86[CHB][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10489815	0.86[CHB][hapmap]
rs10789063	0.84[EUR][1000 genomes]
rs10789064	0.86[CHB][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10789065	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10789066	0.86[CHB][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10789067	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10889098	0.82[ASN][1000 genomes]
rs10889100	0.86[CHB][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10889101	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1109895	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1109896	0.84[CHB][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1114660	0.82[ASN][1000 genomes]
rs11207236	0.81[EUR][1000 genomes]
rs11207237	0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs11207247	0.86[CHB][hapmap]
rs11207248	0.86[CHB][hapmap]
rs11207250	0.86[CHB][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11207251	0.86[CHB][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11207252	0.86[CHB][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11207253	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11207254	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11207262	0.86[CHB][hapmap]
rs1121422	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11581395	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11589236	0.82[CHB][hapmap]
rs11590757	0.86[CHB][hapmap]
rs12030713	1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12058651	0.86[CHB][hapmap]
rs12068196	1.00[CHB][hapmap]
rs12068201	0.86[CHB][hapmap]
rs12070503	0.86[CHB][hapmap]
rs12080357	0.86[CHB][hapmap]
rs12088149	0.81[EUR][1000 genomes]
rs12118488	0.86[CHB][hapmap]
rs12124662	0.81[EUR][1000 genomes]
rs12125391	0.86[CHB][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12139475	0.86[CHB][hapmap]
rs12142098	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12144759	0.86[CHB][hapmap]
rs1388981	0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17117742	0.86[CHB][hapmap]
rs17372425	0.86[CHB][hapmap]
rs17461345	0.82[CHB][hapmap]
rs2087799	0.86[CHB][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs232822	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs232826	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs232827	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs232830	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs232841	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs232842	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs232844	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs232847	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs232848	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs232849	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2406784	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28529311	0.81[EUR][1000 genomes]
rs3087585	0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs3551	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3893156	0.86[CHB][hapmap]
rs486463	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4912195	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4912344	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs525929	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs562166	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs584579	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs602579	0.86[CHB][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs603031	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61779295	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61779296	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs620342	0.86[CHB][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs627218	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6587818	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6587819	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6587820	0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs6587821	0.86[CHB][hapmap]
rs6587828	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs659061	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6656025	0.82[ASN][1000 genomes]
rs6666304	1.00[CHB][hapmap]
rs6667614	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6667703	0.82[ASN][1000 genomes]
rs6679808	0.86[CHB][hapmap]
rs6687324	0.81[EUR][1000 genomes]
rs6690139	0.86[CHB][hapmap]
rs6704300	0.86[CHB][hapmap]
rs672359	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67639631	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7355165	0.86[CHB][hapmap];0.93[EUR][1000 genomes]
rs7355166	0.93[EUR][1000 genomes]
rs7515056	0.86[CHB][hapmap]
rs7517424	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7520008	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7536230	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7536867	0.86[CHB][hapmap]
rs7544032	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7546900	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7547036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs905567	0.86[CHB][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9660901	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[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
rs1775002	TACSTD2	cis	Whole Blood	GTEx
rs1775002	TACSTD2	cis	Thyroid	GTEx
rs1775002	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59012800-59016600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:59012800-59017400	Weak transcription	Pancreas	Pancrea
3	chr1:59012800-59017600	Weak transcription	Aorta	Aorta
4	chr1:59013000-59016600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:59013000-59016600	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:59013000-59016600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:59013200-59017000	Weak transcription	Fetal Brain Male	brain
8	chr1:59014600-59018000	Enhancers	Fetal Lung	lung
9	chr1:59014800-59017400	Weak transcription	Ovary	ovary
10	chr1:59015800-59016800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:59015800-59017800	Enhancers	K562	blood
12	chr1:59016400-59016800	Weak transcription	Fetal Kidney	kidney
13	chr1:59016400-59016800	Enhancers	Placenta	Placenta
14	chr1:59016400-59017400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:59016600-59017000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:59016600-59017000	Enhancers	Brain Hippocampus Middle	brain
17	chr1:59016600-59017200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:59016600-59017200	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr1:59016600-59018000	Enhancers	Fetal Muscle Leg	muscle

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