Variant report

Variant	rs2334960
Chromosome Location	chr3:52066094-52066095
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52050186..52052732-chr3:52065532..52068368,2	MCF-7	breast:
2	chr3:52064203..52066094-chr3:52088910..52090673,2	K562	blood:
3	chr3:52037006..52039861-chr3:52064788..52067442,2	K562	blood:
4	chr3:52058192..52060960-chr3:52064469..52066894,2	K562	blood:
5	chr3:52063502..52067953-chr3:52083827..52087506,5	K562	blood:

Variant related genes	Relation type
ENSG00000164086	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12487108	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492696	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2334959	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821841	0.81[AMR][1000 genomes]
rs4687606	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687609	1.00[YRI][hapmap]
rs4687798	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687799	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66514320	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66530305	0.89[AMR][1000 genomes]
rs6792935	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72622936	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs745618	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs920160	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
9	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52050600-52073400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:52056600-52066400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:52061600-52068600	Enhancers	Fetal Muscle Leg	muscle
4	chr3:52062200-52073800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:52062800-52066800	Weak transcription	Fetal Brain Female	brain
6	chr3:52063000-52066600	Weak transcription	Fetal Brain Male	brain
7	chr3:52063000-52067800	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr3:52063200-52066400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:52063200-52066800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:52063400-52066400	Weak transcription	Fetal Heart	heart
11	chr3:52063600-52066200	Weak transcription	Brain Anterior Caudate	brain
12	chr3:52063600-52066200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:52063600-52067600	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr3:52063600-52072400	Weak transcription	HSMM	muscle
15	chr3:52063800-52066600	Weak transcription	HSMMtube	muscle
16	chr3:52064000-52067400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:52064400-52073600	Weak transcription	Spleen	Spleen
18	chr3:52064800-52067400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:52064800-52067400	Enhancers	Left Ventricle	heart
20	chr3:52065000-52067800	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr3:52065400-52066800	Weak transcription	Psoas Muscle	Psoas
22	chr3:52065400-52068000	Enhancers	Brain Hippocampus Middle	brain
23	chr3:52065600-52066800	Weak transcription	Esophagus	oesophagus
24	chr3:52065600-52067800	Enhancers	Brain Cingulate Gyrus	brain
25	chr3:52065800-52066200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:52065800-52066200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:52065800-52066400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:52065800-52067400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:52065800-52067400	Enhancers	Right Ventricle	heart
30	chr3:52065800-52067600	Enhancers	Right Atrium	heart
31	chr3:52066000-52066400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
32	chr3:52066000-52066800	Enhancers	Brain Substantia Nigra	brain
33	chr3:52066000-52067000	Enhancers	HepG2	liver
34	chr3:52066000-52067200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
35	chr3:52066000-52067600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:52066000-52068000	Enhancers	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links