Variant report

Variant	rs4682840
Chromosome Location	chr3:46982869-46982870
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46979992..46983614-chr3:46988969..46991376,3	MCF-7	breast:
2	chr3:46982362..46985242-chr3:47422135..47423747,2	MCF-7	breast:
3	chr3:46978892..46980837-chr3:46982218..46984599,2	MCF-7	breast:
4	chr3:46974856..46983636-chr3:47025231..47032249,9	K562	blood:

Variant related genes	Relation type
ENSG00000076201	Chromatin interaction
ENSG00000260236	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10461017	0.89[AMR][1000 genomes]
rs10461019	0.89[AMR][1000 genomes]
rs11130108	0.89[AMR][1000 genomes]
rs11130109	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11706212	0.89[AMR][1000 genomes]
rs11708257	0.89[AMR][1000 genomes]
rs11709693	0.89[AMR][1000 genomes]
rs11709876	0.89[AMR][1000 genomes]
rs11713537	0.89[AMR][1000 genomes]
rs11928558	0.89[AMR][1000 genomes]
rs13062185	0.89[AMR][1000 genomes]
rs13082531	0.89[AMR][1000 genomes]
rs1378818	0.89[AMR][1000 genomes]
rs1463394	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1466273	0.91[AFR][1000 genomes]
rs1466274	0.92[AFR][1000 genomes]
rs1869870	0.89[AMR][1000 genomes]
rs2124509	0.89[AMR][1000 genomes]
rs2124510	0.89[AMR][1000 genomes]
rs2385868	0.89[AMR][1000 genomes]
rs2385869	0.89[AMR][1000 genomes]
rs2891887	0.89[AMR][1000 genomes]
rs2891893	0.83[AFR][1000 genomes]
rs4324490	0.89[AMR][1000 genomes]
rs4373094	0.89[AMR][1000 genomes]
rs4378998	0.89[AMR][1000 genomes]
rs4389512	0.89[AMR][1000 genomes]
rs4450857	0.89[AMR][1000 genomes]
rs4478107	0.89[AMR][1000 genomes]
rs4522803	0.89[AMR][1000 genomes]
rs4525902	0.89[AMR][1000 genomes]
rs4543047	0.89[AMR][1000 genomes]
rs4682833	0.89[AMR][1000 genomes]
rs4682835	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4682836	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4682841	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4682843	0.90[AFR][1000 genomes]
rs4683277	0.89[AMR][1000 genomes]
rs4683283	0.89[AMR][1000 genomes]
rs4683284	0.89[AMR][1000 genomes]
rs4683285	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4683286	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4683289	0.92[AFR][1000 genomes]
rs4683290	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4683291	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4683292	0.92[AFR][1000 genomes]
rs4683293	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6442041	0.89[AMR][1000 genomes]
rs6442044	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6442047	0.89[AMR][1000 genomes]
rs6442048	0.89[AMR][1000 genomes]
rs6766676	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6780994	0.89[AMR][1000 genomes]
rs6804732	0.91[AFR][1000 genomes]
rs6806521	0.89[AMR][1000 genomes]
rs7621530	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7624549	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7638549	0.89[AMR][1000 genomes]
rs7646076	0.82[AFR][1000 genomes]
rs7649941	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs936178	0.89[AMR][1000 genomes]
rs936181	0.89[AMR][1000 genomes]
rs936182	0.89[AMR][1000 genomes]
rs936186	0.89[AMR][1000 genomes]
rs9810881	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	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
6	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv3800	chr3:46961648-47007241	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1012682	chr3:46973552-47016357	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46967400-46984400	Genic enhancers	Fetal Intestine Small	intestine
2	chr3:46970800-46984200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:46971200-46988400	Strong transcription	Dnd41	blood
4	chr3:46973800-46985600	Weak transcription	Fetal Kidney	kidney
5	chr3:46974000-46988600	Strong transcription	Primary T cells from cord blood	blood
6	chr3:46975000-46986000	Strong transcription	Thymus	Thymus
7	chr3:46975800-46984800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:46976000-46985600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:46976200-46983200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:46976200-46990200	Weak transcription	Fetal Brain Male	brain
11	chr3:46977000-47000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:46977600-46984200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:46977800-46984400	Genic enhancers	Pancreas	Pancrea
14	chr3:46978000-46984200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:46978000-46990600	Strong transcription	Fetal Stomach	stomach
16	chr3:46978200-46983400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:46978200-46984400	Strong transcription	Hela-S3	cervix
18	chr3:46978200-46985400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:46978400-46983000	Strong transcription	Adipose Nuclei	Adipose
20	chr3:46978400-46984000	Strong transcription	Fetal Brain Female	brain
21	chr3:46978400-46984400	Enhancers	Fetal Heart	heart
22	chr3:46978400-46984600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:46978600-46983000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:46978600-46983400	Strong transcription	NHEK	skin
25	chr3:46978600-46983800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:46978800-46983400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:46978800-46984600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:46979000-46983600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:46979000-46985600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:46979200-46984000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:46979200-46984400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:46979200-46984400	Weak transcription	NH-A	brain
33	chr3:46979400-46983600	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr3:46979400-46984400	Strong transcription	HSMM	muscle
35	chr3:46979400-46989200	Weak transcription	NHDF-Ad	bronchial
36	chr3:46979600-46983200	Strong transcription	Esophagus	oesophagus
37	chr3:46979600-46994600	Genic enhancers	Fetal Thymus	thymus
38	chr3:46979800-46984200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:46979800-46984600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:46980000-46983600	Weak transcription	Psoas Muscle	Psoas
41	chr3:46980200-46984000	Genic enhancers	A549	lung
42	chr3:46980200-46990800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:46980400-46983000	Strong transcription	Fetal Muscle Trunk	muscle
44	chr3:46980600-46983600	Genic enhancers	HepG2	liver
45	chr3:46980600-46985800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:46980800-46983800	Genic enhancers	Right Ventricle	heart
47	chr3:46981000-46984200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr3:46981000-46984400	Genic enhancers	Gastric	stomach
49	chr3:46981200-46983000	Weak transcription	Small Intestine	intestine
50	chr3:46981200-46983200	Strong transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links