Variant report

Variant	rs3796219
Chromosome Location	chr3:191048869-191048870
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:191047769-191049062	Hela-S3	cervix:	n/a	n/a
2	RFX5	chr3:191046576-191049678	Hela-S3	cervix:	n/a	n/a
3	CUX1	chr3:191047969-191048970	K562	blood:	n/a	n/a
4	GTF2F1	chr3:191047516-191048903	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr3:191047937-191050305	PFSK-1	brain:	n/a	n/a
6	RCOR1	chr3:191046379-191049021	Hela-S3	cervix:	n/a	n/a
7	CHD1	chr3:191046720-191049324	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:191046465-191048917	Hela-S3	cervix:	n/a	n/a
9	SMC3	chr3:191047778-191049011	Hela-S3	cervix:	n/a	n/a
10	TBP	chr3:191047805-191049575	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:191046459-191049825	IMR90	lung:	n/a	n/a
12	STAT3	chr3:191048697-191049136	GM12878	blood:	n/a	n/a
13	SMC3	chr3:191048710-191048894	GM12878	blood:	n/a	n/a
14	SMARCC1	chr3:191046178-191049116	Hela-S3	cervix:	n/a	n/a
15	BRCA1	chr3:191047888-191049561	Hela-S3	cervix:	n/a	chr3:191048415-191048422
16	POLR2A	chr3:191046715-191049414	MCF10A-Er-Src	breast:	n/a	n/a
17	TCF7L2	chr3:191047699-191048925	Hela-S3	cervix:	n/a	chr3:191048762-191048778
18	POLR2A	chr3:191048845-191049049	Hela-S3	cervix:	n/a	n/a
19	USF2	chr3:191048764-191048953	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:191046524-191048991	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:191046119-191048998	HepG2	liver:	n/a	n/a
22	RAD21	chr3:191047831-191049236	Hela-S3	cervix:	n/a	n/a
23	RCOR1	chr3:191046313-191048935	K562	blood:	n/a	n/a
24	HCFC1	chr3:191046615-191050300	Hela-S3	cervix:	n/a	n/a
25	CHD2	chr3:191048595-191048912	GM12878	blood:	n/a	n/a
26	WRNIP1	chr3:191047769-191048922	GM12878	blood:	n/a	n/a
27	POLR2A	chr3:191048680-191048944	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:191046203-191049324	PFSK-1	brain:	n/a	n/a
29	CEBPB	chr3:191046462-191049578	Hela-S3	cervix:	n/a	chr3:191049272-191049285 chr3:191048401-191048412 chr3:191049287-191049298 chr3:191049286-191049303 chr3:191049287-191049300
30	MXI1	chr3:191046334-191049099	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:191044441..191046950-chr3:191048340..191050123,2	K562	blood:
2	chr3:191048783..191051594-chr3:191052862..191055527,3	MCF-7	breast:
3	chr3:191040727..191042782-chr3:191048690..191050296,2	K562	blood:
4	chr3:191030743..191032266-chr3:191048762..191051723,2	K562	blood:

Variant related genes	Relation type
UTS2B	TF binding region
ENSG00000152492	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11542549	0.89[ASN][1000 genomes]
rs1435062	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1473869	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1520202	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1520203	0.90[ASN][1000 genomes]
rs1609926	0.87[EUR][1000 genomes]
rs16822378	0.87[EUR][1000 genomes]
rs16822382	0.87[EUR][1000 genomes]
rs16866487	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16866504	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16866505	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17753967	0.84[ASN][1000 genomes]
rs17810246	0.84[ASN][1000 genomes]
rs17810282	0.84[ASN][1000 genomes]
rs17838893	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2056333	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2364379	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs28715898	0.84[ASN][1000 genomes]
rs4677631	0.84[ASN][1000 genomes]
rs4677632	0.84[ASN][1000 genomes]
rs4677725	0.84[ASN][1000 genomes]
rs4677726	0.84[ASN][1000 genomes]
rs4677727	0.84[ASN][1000 genomes]
rs56174842	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57211729	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58141749	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58645265	0.89[ASN][1000 genomes]
rs59709586	0.85[EUR][1000 genomes]
rs61250936	0.82[EUR][1000 genomes]
rs6444541	0.84[ASN][1000 genomes]
rs73185209	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73185210	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73185213	0.89[ASN][1000 genomes]
rs73185226	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73185228	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73185240	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73185255	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73185263	0.87[EUR][1000 genomes]
rs73185284	0.85[EUR][1000 genomes]
rs73185287	0.85[EUR][1000 genomes]
rs73185288	0.85[EUR][1000 genomes]
rs73201627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73201628	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73201630	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73201631	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637196	0.84[ASN][1000 genomes]
rs7642387	0.84[ASN][1000 genomes]
rs7648886	0.84[ASN][1000 genomes]
rs9290986	0.84[ASN][1000 genomes]
rs9823680	0.84[ASN][1000 genomes]
rs9824437	0.84[ASN][1000 genomes]
rs9839751	0.80[ASN][1000 genomes]
rs9843934	0.84[ASN][1000 genomes]
rs9853569	0.84[ASN][1000 genomes]
rs9863255	0.86[ASN][1000 genomes]
rs9876944	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428100	chr3:190793797-191092633	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv878101	chr3:190891939-191059322	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv1851611	chr3:191028147-191073560	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv4169	chr3:191036298-191063465	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv10370	chr3:191046223-191049560	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv980108	chr3:191047936-191051389	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191046200-191049200	Active TSS	Brain Angular Gyrus	brain
2	chr3:191046200-191049800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:191046200-191049800	Active TSS	Stomach Smooth Muscle	stomach
4	chr3:191046400-191049800	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr3:191046600-191049000	Active TSS	Colonic Mucosa	Colon
6	chr3:191046600-191049000	Active TSS	Fetal Intestine Large	intestine
7	chr3:191046600-191049000	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr3:191046600-191049000	Active TSS	Left Ventricle	heart
9	chr3:191046600-191049200	Active TSS	HSMM	muscle
10	chr3:191046600-191049600	Active TSS	HSMMtube	muscle
11	chr3:191046600-191049800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:191046600-191049800	Active TSS	Ovary	ovary
13	chr3:191046600-191049800	Active TSS	Right Ventricle	heart
14	chr3:191046600-191050000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:191046600-191050200	Active TSS	Psoas Muscle	Psoas
16	chr3:191046600-191050600	Active TSS	Aorta	Aorta
17	chr3:191046600-191050600	Active TSS	Right Atrium	heart
18	chr3:191046800-191049000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:191046800-191049000	Active TSS	Lung	lung
20	chr3:191046800-191049000	Active TSS	A549	lung
21	chr3:191046800-191049000	Bivalent/Poised TSS	HepG2	liver
22	chr3:191046800-191049400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:191046800-191049400	Active TSS	Fetal Brain Female	brain
24	chr3:191046800-191049600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:191046800-191049800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:191047000-191049000	Active TSS	Brain Anterior Caudate	brain
27	chr3:191047000-191049200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:191047000-191049200	Active TSS	Muscle Satellite Cultured Cells	--
29	chr3:191047000-191049200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:191047000-191049600	Active TSS	HUVEC	blood vessel
31	chr3:191047000-191049600	Active TSS	NHEK	skin
32	chr3:191047000-191049800	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr3:191047000-191049800	Active TSS	GM12878-XiMat	blood
34	chr3:191047000-191049800	Active TSS	HMEC	breast
35	chr3:191047000-191049800	Active TSS	NHLF	lung
36	chr3:191047600-191049000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:191047600-191049000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr3:191047600-191049600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:191047600-191049800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:191047600-191049800	Active TSS	Brain Germinal Matrix	brain
41	chr3:191047600-191050000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:191047800-191049000	Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr3:191048000-191049000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
44	chr3:191048000-191049200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
45	chr3:191048000-191049200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr3:191048000-191049400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr3:191048000-191050000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:191048200-191049000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
49	chr3:191048200-191049000	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr3:191048200-191049000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links