Variant report

Variant	rs2335929
Chromosome Location	chr3:52498966-52498967
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52498409..52502731-chr3:52503975..52506734,5	MCF-7	breast:
2	chr3:52494660..52496593-chr3:52498409..52500473,3	K562	blood:
3	chr3:52494660..52496410-chr3:52498409..52500473,2	K562	blood:

Variant related genes	Relation type
ENSG00000010322	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1011062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011064	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1035002	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1035003	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865972	0.91[EUR][1000 genomes]
rs11721286	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs123598	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs123603	0.83[EUR][1000 genomes]
rs13074649	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096571	0.80[EUR][1000 genomes]
rs1541495	0.91[EUR][1000 genomes]
rs2109557	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2109558	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2109559	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2215466	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335928	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878549	0.88[EUR][1000 genomes]
rs34827613	0.82[AMR][1000 genomes]
rs3755810	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774409	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs409803	0.81[EUR][1000 genomes]
rs41292858	1.00[AFR][1000 genomes]
rs419050	0.82[AMR][1000 genomes]
rs419604	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs419752	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4312651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687541	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687543	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4687544	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687545	1.00[AFR][1000 genomes]
rs4687614	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687616	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4687617	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4687618	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687619	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687621	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498778	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs575476	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs613519	0.81[EUR][1000 genomes]
rs6414568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445483	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445484	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445485	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445506	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs676034	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771558	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784615	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6787493	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6795333	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6810027	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728408	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs758800	1.00[EUR][1000 genomes]
rs758802	1.00[AFR][1000 genomes]
rs758803	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620015	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs887514	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs929528	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929529	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846089	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9847332	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850471	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855470	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863753	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9867823	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52490800-52499200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:52491400-52500000	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:52491400-52501600	Weak transcription	Right Atrium	heart
4	chr3:52491400-52502200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:52491600-52499600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:52491600-52500000	Strong transcription	Fetal Intestine Large	intestine
7	chr3:52491600-52500600	Strong transcription	Fetal Intestine Small	intestine
8	chr3:52491600-52509400	Weak transcription	Small Intestine	intestine
9	chr3:52491600-52528000	Strong transcription	Thymus	Thymus
10	chr3:52491800-52499400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:52491800-52499400	Strong transcription	Osteobl	bone
12	chr3:52491800-52499600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:52491800-52500000	Strong transcription	Lung	lung
14	chr3:52491800-52500200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:52491800-52502400	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:52491800-52502400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:52491800-52502800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:52491800-52506400	Weak transcription	Stomach Mucosa	stomach
19	chr3:52491800-52517200	Strong transcription	Fetal Stomach	stomach
20	chr3:52491800-52524000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:52491800-52527000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:52491800-52528200	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:52491800-52528200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:52492000-52500000	Strong transcription	Placenta	Placenta
25	chr3:52492000-52500600	Strong transcription	Fetal Muscle Trunk	muscle
26	chr3:52492000-52502400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:52492000-52502600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr3:52492000-52503400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:52492000-52516800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:52492000-52517200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:52492200-52506200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:52492400-52517400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:52493000-52499400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:52493000-52502800	Strong transcription	Dnd41	blood
35	chr3:52493000-52506800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr3:52493000-52527800	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr3:52493200-52499400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:52493200-52500800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr3:52493200-52507000	Strong transcription	Fetal Thymus	thymus
40	chr3:52493400-52499200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:52493400-52499200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:52493400-52499400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr3:52493400-52499400	Weak transcription	A549	lung
44	chr3:52493400-52499800	Weak transcription	Fetal Heart	heart
45	chr3:52493400-52502200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr3:52493400-52504800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr3:52493400-52505000	Weak transcription	Brain Substantia Nigra	brain
48	chr3:52493400-52505800	Weak transcription	Psoas Muscle	Psoas
49	chr3:52493400-52506000	Weak transcription	Hela-S3	cervix
50	chr3:52493400-52506000	Weak transcription	K562	blood

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