Variant report

Variant	rs4683294
Chromosome Location	chr3:46979013-46979014
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46967009..46980239-chr3:47015804..47024437,23	MCF-7	breast:
2	chr3:46974856..46983636-chr3:47025231..47032249,9	K562	blood:
3	chr3:46978892..46980837-chr3:46982218..46984599,2	MCF-7	breast:
4	chr3:46975584..46977390-chr3:46978479..46982012,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160796	Chromatin interaction
ENSG00000160799	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2290546	0.91[CEU][hapmap]
rs4587	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4683296	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4683297	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4683298	0.84[CEU][hapmap]
rs6442038	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs6442040	0.84[CEU][hapmap]
rs6780601	0.81[EUR][1000 genomes]
rs7623898	0.81[EUR][1000 genomes]
rs7645278	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs9852082	0.95[CEU][hapmap];0.81[EUR][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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4683294	LZTFL1	cis	parietal	SCAN
rs4683294	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs4683294	SCAP	cis	parietal	SCAN
rs4683294	CCDC12	cis	cerebellum	SCAN
rs4683294	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs4683294	SCAP	cis	cerebellum	SCAN

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	chr3:46970800-46979400	Enhancers	HUVEC	blood vessel
3	chr3:46970800-46984200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:46971200-46988400	Strong transcription	Dnd41	blood
5	chr3:46971800-46980000	Enhancers	Psoas Muscle	Psoas
6	chr3:46971800-46982800	Enhancers	Right Atrium	heart
7	chr3:46972400-46981200	Genic enhancers	Fetal Muscle Leg	muscle
8	chr3:46973800-46982400	Genic enhancers	Primary B cells from peripheral blood	blood
9	chr3:46973800-46985600	Weak transcription	Fetal Kidney	kidney
10	chr3:46974000-46988600	Strong transcription	Primary T cells from cord blood	blood
11	chr3:46974200-46979200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr3:46975000-46979400	Genic enhancers	NHLF	lung
13	chr3:46975000-46986000	Strong transcription	Thymus	Thymus
14	chr3:46975600-46979200	Enhancers	NH-A	brain
15	chr3:46975600-46982800	Genic enhancers	Fetal Intestine Large	intestine
16	chr3:46975800-46984800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr3:46976000-46979200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:46976000-46985600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:46976200-46980400	Genic enhancers	Fetal Muscle Trunk	muscle
20	chr3:46976200-46980600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:46976200-46982400	Genic enhancers	Spleen	Spleen
22	chr3:46976200-46983200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:46976200-46990200	Weak transcription	Fetal Brain Male	brain
24	chr3:46976400-46979600	Strong transcription	GM12878-XiMat	blood
25	chr3:46976800-46979600	Strong transcription	Fetal Thymus	thymus
26	chr3:46977000-46980600	Weak transcription	Aorta	Aorta
27	chr3:46977000-46982800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:46977000-47000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:46977200-46979600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:46977200-46981600	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:46977200-46982800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:46977400-46979600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr3:46977400-46982000	Genic enhancers	Stomach Smooth Muscle	stomach
34	chr3:46977400-46982800	Genic enhancers	Placenta	Placenta
35	chr3:46977400-46982800	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr3:46977600-46979200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:46977600-46979200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:46977600-46979200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr3:46977600-46979200	Genic enhancers	Osteobl	bone
40	chr3:46977600-46979400	Genic enhancers	Muscle Satellite Cultured Cells	--
41	chr3:46977600-46979400	Genic enhancers	HSMM	muscle
42	chr3:46977600-46979600	Genic enhancers	Liver	Liver
43	chr3:46977600-46979600	Genic enhancers	Brain Inferior Temporal Lobe	brain
44	chr3:46977600-46981600	Weak transcription	Ovary	ovary
45	chr3:46977600-46982200	Genic enhancers	Lung	lung
46	chr3:46977600-46982600	Strong transcription	Brain Germinal Matrix	brain
47	chr3:46977600-46984200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:46977800-46979200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr3:46977800-46979400	Genic enhancers	A549	lung
50	chr3:46977800-46979400	Genic enhancers	NHDF-Ad	bronchial

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