Variant report

Variant	rs929528
Chromosome Location	chr3:52505445-52505446
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:52505260-52505855	MCF-7	breast:	n/a	n/a
2	EP300	chr3:52505436-52505930	T-47D	breast:	n/a	n/a
3	POLR2A	chr3:52505430-52505843	GM12892	blood:	n/a	n/a
4	POLR2A	chr3:52504670-52505761	GM12878	blood:	n/a	n/a
5	CTCF	chr3:52505380-52505530	SK-N-SH_RA	brain:	n/a	n/a
6	POLR2A	chr3:52504957-52505665	GM12892	blood:	n/a	n/a
7	GATA3	chr3:52505278-52505878	MCF-7	breast:	n/a	n/a
8	FOXA1	chr3:52505356-52505854	T-47D	breast:	n/a	chr3:52505740-52505755
9	POLR2A	chr3:52505416-52505594	HepG2	liver:	n/a	n/a
10	MYC	chr3:52505404-52505466	MCF-7	breast:	n/a	n/a
11	POLR2A	chr3:52505247-52505557	H1-hESC	embryonic stem cell:	n/a	n/a
12	MYC	chr3:52505325-52505830	MCF-7	breast:	n/a	n/a
13	POLR2A	chr3:52505398-52505780	MCF-7	breast:	n/a	n/a
14	POLR2A	chr3:52505323-52505571	MCF-7	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52487939..52491238-chr3:52504089..52507877,6	MCF-7	breast:
2	chr3:52505024..52507887-chr3:52527744..52529874,2	MCF-7	breast:
3	chr3:52503525..52506168-chr3:52566167..52568849,2	MCF-7	breast:
4	chr3:52505027..52507504-chr3:52738535..52741338,2	MCF-7	breast:
5	chr3:52504996..52506918-chr3:52535565..52538055,2	MCF-7	breast:
6	chr3:52504515..52506973-chr3:52565446..52568302,2	MCF-7	breast:

No data

Variant related genes	Relation type
NISCH	TF binding region
ENSG00000016864	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000114902	Chromatin interaction
ENSG00000010327	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000168268	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1011062	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011063	1.00[JPT][hapmap]
rs1011064	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];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]
rs1077142	1.00[JPT][hapmap]
rs10865972	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs11707864	1.00[JPT][hapmap]
rs11707931	1.00[JPT][hapmap]
rs11709658	1.00[JPT][hapmap]
rs11711934	1.00[JPT][hapmap]
rs11714402	1.00[JPT][hapmap]
rs11716017	1.00[JPT][hapmap]
rs11718125	1.00[JPT][hapmap]
rs11721286	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs123598	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs123602	1.00[JPT][hapmap]
rs123603	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs13059674	1.00[JPT][hapmap]
rs13060192	1.00[JPT][hapmap]
rs13071708	1.00[JPT][hapmap]
rs13074649	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075370	1.00[JPT][hapmap]
rs13076508	1.00[JPT][hapmap]
rs13076890	1.00[JPT][hapmap]
rs13091360	1.00[JPT][hapmap]
rs13091545	1.00[JPT][hapmap]
rs13096571	0.80[EUR][1000 genomes]
rs1541495	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs17052058	1.00[JPT][hapmap]
rs17052061	1.00[JPT][hapmap]
rs17052068	1.00[JPT][hapmap]
rs2016575	1.00[JPT][hapmap]
rs2109557	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2109558	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2109559	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2159607	1.00[JPT][hapmap]
rs2215466	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335640	1.00[JPT][hapmap]
rs2335928	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335929	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878549	1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs34762015	1.00[JPT][hapmap]
rs34827613	0.82[AMR][1000 genomes]
rs35860312	1.00[JPT][hapmap]
rs3755810	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774409	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774410	1.00[JPT][hapmap]
rs3796343	1.00[JPT][hapmap]
rs390802	1.00[JPT][hapmap]
rs409803	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs419050	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs419604	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs419752	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4312651	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687541	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687543	0.85[EUR][1000 genomes]
rs4687544	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687614	1.00[CEU][hapmap];1.00[JPT][hapmap];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[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4687618	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687619	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687621	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498778	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs498946	1.00[JPT][hapmap]
rs575476	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs613519	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs634382	1.00[JPT][hapmap]
rs6414568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445386	1.00[JPT][hapmap]
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[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445506	1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs676034	1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763882	1.00[JPT][hapmap]
rs6771558	1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782162	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784615	1.00[JPT][hapmap];1.00[AFR][1000 genomes];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]
rs6796333	1.00[JPT][hapmap]
rs6800707	1.00[JPT][hapmap]
rs6810027	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728408	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs758800	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs758803	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620015	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs82825	1.00[JPT][hapmap]
rs887514	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs887515	1.00[JPT][hapmap]
rs929529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9844183	1.00[JPT][hapmap]
rs9846089	1.00[CEU][hapmap];1.00[JPT][hapmap];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	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855470	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863753	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9867823	1.00[CEU][hapmap];1.00[JPT][hapmap];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	chr3:52491600-52509400	Weak transcription	Small Intestine	intestine
2	chr3:52491600-52528000	Strong transcription	Thymus	Thymus
3	chr3:52491800-52506400	Weak transcription	Stomach Mucosa	stomach
4	chr3:52491800-52517200	Strong transcription	Fetal Stomach	stomach
5	chr3:52491800-52524000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:52491800-52527000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:52491800-52528200	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:52491800-52528200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:52492000-52516800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:52492000-52517200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:52492200-52506200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:52492400-52517400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:52493000-52506800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:52493000-52527800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr3:52493200-52507000	Strong transcription	Fetal Thymus	thymus
16	chr3:52493400-52505800	Weak transcription	Psoas Muscle	Psoas
17	chr3:52493400-52506000	Weak transcription	Hela-S3	cervix
18	chr3:52493400-52506000	Weak transcription	K562	blood
19	chr3:52493400-52506400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:52495400-52507600	Weak transcription	Fetal Kidney	kidney
21	chr3:52495600-52506200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:52497400-52505600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr3:52498000-52506400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:52498600-52527200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr3:52499200-52505600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr3:52499200-52517200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr3:52499400-52527800	Strong transcription	Primary T cells from cord blood	blood
28	chr3:52499600-52529200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr3:52499800-52507200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:52500200-52517000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:52501000-52515200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:52501600-52528800	Strong transcription	Fetal Intestine Small	intestine
33	chr3:52502400-52506000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:52502800-52506000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:52502800-52506000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr3:52502800-52506400	Weak transcription	NHDF-Ad	bronchial
37	chr3:52502800-52517200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:52503200-52505600	Strong transcription	Brain Anterior Caudate	brain
39	chr3:52503200-52506400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr3:52503400-52506200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:52503400-52517200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:52503600-52507600	Weak transcription	Fetal Brain Male	brain
43	chr3:52504200-52505800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr3:52504200-52517200	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr3:52504200-52526600	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr3:52504200-52526800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:52504200-52527400	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:52504200-52527400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:52504200-52527600	Strong transcription	Dnd41	blood
50	chr3:52504200-52527800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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