Variant report

Variant	rs807937
Chromosome Location	chr3:47323000-47323001
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr3:47322954-47325702	K562	blood:	n/a	chr3:47325141-47325149
2	POLR2A	chr3:47321384-47325284	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr3:47321796-47324876	Hela-S3	cervix:	n/a	n/a
4	SIN3AK20	chr3:47322971-47323501	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr3:47322145-47323720	A549	lung:	n/a	n/a
6	POLR2A	chr3:47322096-47324639	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr3:47322067-47324681	IMR90	lung:	n/a	n/a
8	TBP	chr3:47322977-47323586	K562	blood:	n/a	n/a
9	HEY1	chr3:47322979-47324694	K562	blood:	n/a	n/a
10	POLR2A	chr3:47322881-47323156	HepG2	liver:	n/a	n/a
11	RPC155	chr3:47322604-47323318	Hela-S3	cervix:	n/a	n/a
12	MXI1	chr3:47322515-47325911	SK-N-SH	brain:	n/a	n/a
13	CBX3	chr3:47322986-47325049	K562	blood:	n/a	n/a
14	POLR2A	chr3:47321218-47324899	MCF10A-Er-Src	breast:	n/a	n/a
15	CTCF	chr3:47322922-47324141	SK-N-SH	brain:	n/a	chr3:47323233-47323242
16	CTCF	chr3:47322961-47323554	K562	blood:	n/a	chr3:47323233-47323242
17	CTCF	chr3:47322971-47323036	Kidney_OC	kidney:	n/a	n/a
18	NR2F2	chr3:47322945-47325529	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:47306715..47308916-chr3:47322571..47324674,2	MCF-7	breast:
2	chr3:47290764..47292267-chr3:47322907..47324747,2	K562	blood:
3	chr3:47321814..47325452-chr3:47418885..47424380,8	K562	blood:
4	chr3:47318429..47320664-chr3:47321864..47324822,2	MCF-7	breast:
5	chr3:47016936..47018509-chr3:47322606..47324747,2	K562	blood:
6	chr3:47204122..47207133-chr3:47321636..47325818,4	K562	blood:
7	chr3:47322971..47323489-chr3:47365701..47366462,2	MCF-7	breast:

No data

Variant related genes	Relation type
KLHL18	TF binding region
KIF9	TF binding region
ENSG00000160799	Chromatin interaction
ENSG00000076201	Chromatin interaction
ENSG00000088727	Chromatin interaction
ENSG00000181555	Chromatin interaction
ENSG00000239128	Chromatin interaction
ENSG00000227398	Chromatin interaction
ENSG00000260236	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1076394	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130123	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11130124	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130126	0.86[EUR][1000 genomes]
rs11710013	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11710322	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11714294	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11915074	0.86[EUR][1000 genomes]
rs11920853	0.86[EUR][1000 genomes]
rs11921117	0.85[EUR][1000 genomes]
rs13072802	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13094438	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1638676	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17476234	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276853	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2276854	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs295441	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs295442	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683326	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59689369	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6768221	0.86[EUR][1000 genomes]
rs6791842	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7636423	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs807932	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs807935	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs807936	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs811115	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1014457	chr3:47222292-47335175	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv536560	chr3:47222292-47335175	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs807937	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs807937	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:149 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47293600-47323200	Weak transcription	Spleen	Spleen
2	chr3:47301200-47323000	Weak transcription	Psoas Muscle	Psoas
3	chr3:47302800-47323200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:47305600-47323200	Weak transcription	Primary T cells from cord blood	blood
5	chr3:47308600-47323000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:47308600-47323200	Weak transcription	Esophagus	oesophagus
7	chr3:47308800-47323000	Weak transcription	Adipose Nuclei	Adipose
8	chr3:47308800-47323000	Weak transcription	Brain Substantia Nigra	brain
9	chr3:47309000-47323000	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:47309000-47323200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:47309000-47323200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:47309200-47323200	Weak transcription	HSMMtube	muscle
13	chr3:47312400-47323000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:47314800-47323200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:47316200-47323000	Weak transcription	Fetal Stomach	stomach
16	chr3:47316200-47323200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:47317800-47323000	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:47321400-47323200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:47321800-47323000	Enhancers	Pancreas	Pancrea
20	chr3:47322200-47323000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:47322200-47323000	Enhancers	Gastric	stomach
22	chr3:47322200-47323000	Enhancers	Stomach Smooth Muscle	stomach
23	chr3:47322200-47323000	Enhancers	Dnd41	blood
24	chr3:47322200-47323200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr3:47322200-47323200	Enhancers	GM12878-XiMat	blood
26	chr3:47322200-47323400	Enhancers	Lung	lung
27	chr3:47322400-47323000	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr3:47322400-47323000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:47322400-47323000	Enhancers	Placenta	Placenta
30	chr3:47322400-47323000	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr3:47322400-47323200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:47322400-47323200	Enhancers	Primary hematopoietic stem cells	blood
33	chr3:47322400-47323200	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr3:47322400-47323200	Weak transcription	Aorta	Aorta
35	chr3:47322400-47323200	Weak transcription	Brain Germinal Matrix	brain
36	chr3:47322400-47323200	Enhancers	Right Ventricle	heart
37	chr3:47322400-47323200	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr3:47322400-47323200	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr3:47322400-47323600	Flanking Active TSS	NHEK	skin
40	chr3:47322600-47323000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:47322600-47323000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:47322600-47323000	Enhancers	Brain Anterior Caudate	brain
43	chr3:47322600-47323000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:47322600-47323000	Weak transcription	Fetal Brain Female	brain
45	chr3:47322600-47323000	Flanking Active TSS	A549	lung
46	chr3:47322600-47323000	Flanking Active TSS	HMEC	breast
47	chr3:47322600-47323000	Enhancers	NHDF-Ad	bronchial
48	chr3:47322600-47323000	Enhancers	Osteobl	bone
49	chr3:47322600-47323200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr3:47322600-47323200	Enhancers	Primary monocytes fromperipheralblood	blood

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