Variant report

Variant	rs3743604
Chromosome Location	chr16:75606360-75606361
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:75606264-75606413	K562	blood:	n/a	n/a
2	SPI1	chr16:75605649-75606416	GM12878	blood:	n/a	n/a
3	MTA3	chr16:75605841-75606618	GM12878	blood:	n/a	n/a
4	RUNX3	chr16:75605727-75606450	GM12878	blood:	n/a	n/a
5	POU2F2	chr16:75605787-75606397	GM12878	blood:	n/a	n/a
6	RUNX3	chr16:75605793-75606511	GM12878	blood:	n/a	n/a
7	MTA3	chr16:75605769-75606558	GM12878	blood:	n/a	n/a
8	POLR2A	chr16:75606106-75607581	GM12878	blood:	n/a	n/a
9	POLR2A	chr16:75606199-75606443	K562	blood:	n/a	n/a
10	STAT5A	chr16:75605796-75606540	GM12878	blood:	n/a	chr16:75606490-75606501 chr16:75606398-75606410
11	BCLAF1	chr16:75605777-75606509	GM12878	blood:	n/a	n/a
12	POLR2A	chr16:75606080-75606458	K562	blood:	n/a	n/a
13	POLR2A	chr16:75606062-75606436	K562	blood:	n/a	n/a
14	POLR2A	chr16:75606220-75606509	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr16:75606045-75606480	GM12878	blood:	n/a	n/a
16	USF2	chr16:75606233-75606364	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr16:75605349..75607916-chr16:75609968..75612593,3	MCF-7	breast:
2	chr16:75598960..75602885-chr16:75604556..75608989,5	K562	blood:
3	chr16:75602668..75604551-chr16:75605865..75608375,2	MCF-7	breast:
4	chr16:75606093..75608487-chr16:75610789..75613227,2	MCF-7	breast:
5	chr16:75599241..75602314-chr16:75606211..75609238,3	MCF-7	breast:
6	chr16:75605676..75608554-chr16:75681140..75683398,2	K562	blood:

No data

Variant related genes	Relation type
GABARAPL2	TF binding region
ENSG00000166848	Chromatin interaction
ENSG00000065427	Chromatin interaction
ENSG00000034713	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11149840	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11149841	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11641024	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11642599	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11642713	0.86[AFR][1000 genomes]
rs11644468	0.84[EUR][1000 genomes]
rs11645180	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11649388	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12149103	0.82[EUR][1000 genomes]
rs12149626	0.81[EUR][1000 genomes]
rs34270346	0.82[EUR][1000 genomes]
rs3743602	0.81[AMR][1000 genomes]
rs3784932	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3826107	0.89[EUR][1000 genomes]
rs4149500	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4149501	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4149504	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4485400	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59359930	0.88[EUR][1000 genomes]
rs60988480	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7202717	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7206481	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs74024804	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8046531	0.88[EUR][1000 genomes]
rs8046977	0.88[EUR][1000 genomes]
rs8048818	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv1065995	chr16:75373756-75626027	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv1063718	chr16:75395969-75608071	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	nsv525955	chr16:75473332-75628345	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
6	nsv532561	chr16:75519574-75636977	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3743604	ADAT1	cis	Artery Tibial	GTEx
rs3743604	ADAT1	cis	lung	GTEx
rs3743604	ADAT1	Cis_1M	lymphoblastoid	RTeQTL
rs3743604	ADAT1	cis	Esophagus Muscularis	GTEx
rs3743604	ADAT1	cis	Adipose Subcutaneous	GTEx
rs3743604	ADAT1	cis	Skin Sun Exposed Lower leg	GTEx
rs3743604	ADAT1	cis	Thyroid	GTEx
rs3743604	ADAT1	cis	Nerve Tibial	GTEx
rs3743604	ADAT1	cis	multi-tissue	Pritchard
rs3743604	ADAT1	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75601200-75608600	Genic enhancers	Primary B cells from peripheral blood	blood
2	chr16:75601200-75624400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr16:75601400-75607200	Genic enhancers	Primary T cells fromperipheralblood	blood
4	chr16:75601400-75610200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr16:75601600-75608800	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr16:75601600-75609600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr16:75601600-75613400	Strong transcription	NH-A	brain
8	chr16:75601600-75613800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr16:75601600-75613800	Strong transcription	A549	lung
10	chr16:75601600-75614400	Genic enhancers	Brain Anterior Caudate	brain
11	chr16:75601600-75615200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr16:75601600-75615400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr16:75601800-75608400	Genic enhancers	Left Ventricle	heart
14	chr16:75601800-75608400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
15	chr16:75601800-75608400	Strong transcription	Hela-S3	cervix
16	chr16:75601800-75608400	Strong transcription	NHDF-Ad	bronchial
17	chr16:75601800-75608800	Strong transcription	H9 Cell Line	embryonic stem cell
18	chr16:75601800-75608800	Genic enhancers	Brain Hippocampus Middle	brain
19	chr16:75601800-75608800	Strong transcription	HUVEC	blood vessel
20	chr16:75601800-75609000	Strong transcription	NHEK	skin
21	chr16:75601800-75609400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr16:75601800-75609800	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr16:75601800-75609800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr16:75601800-75612000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr16:75601800-75612800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr16:75601800-75614400	Strong transcription	Thymus	Thymus
27	chr16:75601800-75615400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr16:75602000-75609200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr16:75602000-75612400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr16:75602000-75612800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr16:75602000-75613200	Strong transcription	HepG2	liver
32	chr16:75602000-75613200	Strong transcription	NHLF	lung
33	chr16:75602000-75613600	Strong transcription	Placenta Amnion	Placenta Amnion
34	chr16:75602000-75614000	Strong transcription	Fetal Lung	lung
35	chr16:75602000-75614200	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr16:75602000-75614200	Strong transcription	Osteobl	bone
37	chr16:75602000-75614400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr16:75602000-75614600	Strong transcription	Placenta	Placenta
39	chr16:75602000-75615000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr16:75602000-75615200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr16:75602200-75606800	Genic enhancers	Adipose Nuclei	Adipose
42	chr16:75602200-75608400	Genic enhancers	Brain Cingulate Gyrus	brain
43	chr16:75602200-75609000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr16:75602200-75609400	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr16:75602200-75610400	Strong transcription	HSMM	muscle
46	chr16:75602200-75614400	Strong transcription	Fetal Intestine Large	intestine
47	chr16:75602200-75614800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr16:75602400-75606400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr16:75602400-75609000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
50	chr16:75602600-75608400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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