Variant report

Variant	rs3743605
Chromosome Location	chr16:75606387-75606388
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 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

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
ENSG00000034713	Chromatin interaction
ENSG00000065427	Chromatin interaction
ENSG00000166848	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11149842	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12445389	0.83[AMR][1000 genomes]
rs12445937	0.83[AMR][1000 genomes]
rs12446652	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12595883	0.89[AMR][1000 genomes]
rs12596033	0.88[AMR][1000 genomes]
rs12596724	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12596857	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12598094	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12598741	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12598751	0.89[AMR][1000 genomes]
rs12599212	0.89[AMR][1000 genomes]
rs12599322	0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12600066	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12600271	0.94[AMR][1000 genomes]
rs16940253	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16940467	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16941533	0.81[ASN][1000 genomes]
rs17697211	0.89[AMR][1000 genomes]
rs17764821	0.84[AMR][1000 genomes]
rs1812507	0.89[AMR][1000 genomes]
rs1836547	0.85[AMR][1000 genomes]
rs1979717	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2082751	0.82[ASN][1000 genomes]
rs2164245	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2242406	0.91[AMR][1000 genomes]
rs2278469	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2289063	0.88[AMR][1000 genomes]
rs2903106	0.84[ASN][1000 genomes]
rs3736377	0.84[AMR][1000 genomes]
rs3743599	0.88[AMR][1000 genomes]
rs3743601	0.89[AMR][1000 genomes]
rs3743603	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3851741	0.85[AMR][1000 genomes]
rs41505349	0.84[ASN][1000 genomes]
rs4887833	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4888436	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4888437	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4888440	0.88[AMR][1000 genomes]
rs4888442	0.89[AMR][1000 genomes]
rs5010692	0.86[ASN][1000 genomes]
rs57252551	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57396453	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs58273293	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58508930	0.88[AMR][1000 genomes]
rs58597869	0.93[AMR][1000 genomes]
rs58673511	0.84[AMR][1000 genomes]
rs58719566	0.94[AMR][1000 genomes]
rs59907199	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60393074	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs60952428	0.84[AMR][1000 genomes]
rs61036571	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61078946	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61539645	0.82[AMR][1000 genomes]
rs6564268	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7186966	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7187672	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7193066	0.84[AMR][1000 genomes]
rs7195338	0.88[AMR][1000 genomes]
rs719574	0.87[AMR][1000 genomes]
rs7206799	0.89[AMR][1000 genomes]
rs73615030	0.88[ASN][1000 genomes]
rs74027438	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7499759	0.93[AMR][1000 genomes]
rs8051241	0.93[ASN][1000 genomes]
rs8051713	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8056968	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8060972	0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8061505	0.82[ASN][1000 genomes]
rs8192516	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs963820	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9788802	0.88[AMR][1000 genomes]
rs9934159	0.87[AMR][1000 genomes];0.92[ASN][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

No data

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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