Variant report

Variant	rs334540
Chromosome Location	chr3:119826506-119826507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119812621..119817617-chr3:119824950..119830930,7	K562	blood:
2	chr3:119817451..119819097-chr3:119825949..119828864,2	K562	blood:
3	chr3:119825155..119827767-chr3:119838383..119840423,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs182839	0.87[AMR][1000 genomes]
rs184576	0.90[EUR][1000 genomes]
rs2035672	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2035673	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2035674	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2171599	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28398784	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3112282	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3112283	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs334534	0.87[AMR][1000 genomes]
rs334538	0.88[ASN][1000 genomes]
rs334539	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs334545	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs334549	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs334551	0.80[AMR][1000 genomes]
rs334552	0.87[AMR][1000 genomes]
rs334554	0.87[AMR][1000 genomes]
rs334561	0.87[AMR][1000 genomes]
rs6438558	0.83[EUR][1000 genomes]
rs6781470	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6805931	0.87[AMR][1000 genomes]
rs7644268	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs901920	0.83[EUR][1000 genomes]
rs923380	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv3964	chr3:119786623-119831698	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
6	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119814600-119830600	Weak transcription	Gastric	stomach
2	chr3:119815000-119829200	Weak transcription	Ovary	ovary
3	chr3:119815400-119828000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:119815400-119828200	Weak transcription	Aorta	Aorta
5	chr3:119815400-119828800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:119815400-119830000	Weak transcription	Fetal Lung	lung
7	chr3:119815800-119829000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr3:119816000-119827400	Weak transcription	Thymus	Thymus
9	chr3:119816000-119828600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:119816000-119829000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:119816200-119831000	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:119816200-119832600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:119816400-119826600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:119816400-119826600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:119816400-119831400	Weak transcription	Brain Substantia Nigra	brain
16	chr3:119818000-119831800	Weak transcription	HSMM	muscle
17	chr3:119818200-119828600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:119818600-119831800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:119819000-119828600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:119819800-119827400	Weak transcription	Fetal Thymus	thymus
21	chr3:119819800-119832400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:119820000-119832200	Weak transcription	HSMMtube	muscle
23	chr3:119820200-119828200	Weak transcription	NHDF-Ad	bronchial
24	chr3:119820200-119832000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:119820600-119827400	Weak transcription	Fetal Intestine Small	intestine
26	chr3:119820600-119829400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:119821400-119832000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:119822000-119827000	Weak transcription	Osteobl	bone
29	chr3:119822000-119829400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:119822000-119830200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:119822000-119831800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:119822000-119835200	Weak transcription	Psoas Muscle	Psoas
33	chr3:119822200-119829800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:119822200-119830600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:119822200-119830800	Weak transcription	Pancreas	Pancrea
36	chr3:119822200-119831000	Weak transcription	Esophagus	oesophagus
37	chr3:119822400-119827200	Weak transcription	HMEC	breast
38	chr3:119822400-119828200	Weak transcription	Right Ventricle	heart
39	chr3:119822400-119830600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:119822400-119831800	Weak transcription	Liver	Liver
41	chr3:119822600-119829600	Weak transcription	Fetal Brain Male	brain
42	chr3:119822600-119831800	Weak transcription	A549	lung
43	chr3:119825200-119827400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:119825200-119829400	Weak transcription	NHEK	skin
45	chr3:119825200-119829800	Weak transcription	Placenta	Placenta
46	chr3:119826000-119829400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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