Variant report

Variant	rs4683276
Chromosome Location	chr3:47040695-47040696
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:47040560-47040710	GM12874	blood:	n/a	n/a
2	POLR2A	chr3:47040648-47040883	GM12878	blood:	n/a	n/a
3	CTCF	chr3:47040660-47040810	SAEC	small airway:	n/a	n/a
4	POLR2A	chr3:47036080-47042185	GM12892	blood:	n/a	n/a
5	CTCF	chr3:47040580-47040730	AG10803	skin:	n/a	n/a
6	POLR2A	chr3:47040597-47042121	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:47040670-47041997	K562	blood:	n/a	n/a
8	POLR2A	chr3:47040676-47041764	K562	blood:	n/a	n/a
9	RAD21	chr3:47039695-47040697	SK-N-SH	brain:	n/a	chr3:47039926-47039938 chr3:47040624-47040634

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:46951368..46952262-chr3:47039779..47040735,3	K562	blood:
2	chr3:47038738..47041744-chr3:47049789..47052323,3	MCF-7	breast:
3	chr3:46964655..46965958-chr3:47039692..47040743,10	K562	blood:
4	chr3:46964881..46965821-chr3:47039447..47041043,9	MCF-7	breast:
5	chr3:46746385..46747067-chr3:47040079..47041127,4	K562	blood:
6	chr3:47028237..47028761-chr3:47040210..47040750,2	K562	blood:
7	chr3:47039305..47042049-chr3:47322741..47325058,3	K562	blood:

No data

Variant related genes	Relation type
NBEAL2	TF binding region
ENSG00000114648	Chromatin interaction
ENSG00000088727	Chromatin interaction
ENSG00000160799	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12485582	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12486248	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12489851	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491419	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12497141	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17079425	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305640	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35201996	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3816531	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60285825	0.87[AMR][1000 genomes]
rs61364027	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7372834	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1009396	chr3:46994991-47048166	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	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
7	esv1800172	chr3:47013346-47049306	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv590209	chr3:47018214-47050784	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
9	nsv876757	chr3:47018214-47058057	Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47022400-47041600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:47022400-47041800	Weak transcription	Brain Germinal Matrix	brain
3	chr3:47022400-47042000	Weak transcription	Brain Substantia Nigra	brain
4	chr3:47022600-47049000	Weak transcription	Hela-S3	cervix
5	chr3:47022600-47050600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:47023200-47042000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:47029800-47040800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:47029800-47040800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:47029800-47041000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:47029800-47042000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:47029800-47042400	Weak transcription	Small Intestine	intestine
12	chr3:47029800-47042600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:47029800-47050600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:47030200-47044600	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:47030800-47045600	Weak transcription	Aorta	Aorta
16	chr3:47031000-47041800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:47031000-47049600	Strong transcription	Gastric	stomach
18	chr3:47031000-47050200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:47031000-47053000	Strong transcription	Dnd41	blood
20	chr3:47031800-47043400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:47032000-47041800	Weak transcription	HUVEC	blood vessel
22	chr3:47032000-47042400	Strong transcription	Lung	lung
23	chr3:47032200-47041000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:47032200-47050000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:47033200-47042400	Weak transcription	Fetal Brain Female	brain
26	chr3:47033800-47049200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr3:47034200-47049800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr3:47035400-47049000	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:47036000-47040800	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:47036600-47041200	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:47036800-47042000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:47036800-47044200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:47037000-47040800	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:47037000-47041800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:47037200-47040800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr3:47037200-47040800	Weak transcription	Liver	Liver
37	chr3:47037200-47041600	Weak transcription	Left Ventricle	heart
38	chr3:47037400-47042400	Weak transcription	Brain Anterior Caudate	brain
39	chr3:47037400-47042800	Genic enhancers	Primary T cells fromperipheralblood	blood
40	chr3:47037400-47043000	Weak transcription	Primary B cells from cord blood	blood
41	chr3:47038000-47050000	Strong transcription	Thymus	Thymus
42	chr3:47038200-47041800	Weak transcription	NHLF	lung
43	chr3:47038400-47041000	Genic enhancers	Fetal Thymus	thymus
44	chr3:47038600-47044400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:47038600-47044600	Strong transcription	K562	blood
46	chr3:47038600-47050000	Strong transcription	Fetal Stomach	stomach
47	chr3:47038600-47050400	Weak transcription	Fetal Lung	lung
48	chr3:47038800-47040800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr3:47038800-47041600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:47038800-47041600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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