Variant report

Variant	rs3755810
Chromosome Location	chr3:52487100-52487101
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr3:52486592-52487164	ECC-1	luminal epithelium:	n/a	chr3:52486724-52486739 chr3:52486755-52486770
2	ZBTB7A	chr3:52486533-52487484	ECC-1	luminal epithelium:	n/a	n/a
3	ESR1	chr3:52486560-52487120	ECC-1	luminal epithelium:	n/a	chr3:52486724-52486739 chr3:52486755-52486770
4	ESR1	chr3:52486490-52487109	ECC-1	luminal epithelium:	n/a	chr3:52486724-52486739 chr3:52486755-52486770
5	EGR1	chr3:52486644-52487180	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52481830..52487806-chr3:52487911..52490298,8	K562	blood:
2	chr3:52486786..52490623-chr3:52738506..52740742,3	MCF-7	breast:
3	chr3:52312419..52314160-chr3:52485786..52488594,2	MCF-7	breast:

Variant related genes	Relation type
TNNC1	TF binding region
NISCH	TF binding region
ENSG00000010322	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000114902	Chromatin interaction
ENSG00000016864	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1011062	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011064	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1035002	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1035003	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1077142	1.00[CHD][hapmap]
rs10865972	0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs11707864	1.00[CHD][hapmap]
rs11714402	1.00[CHD][hapmap]
rs11718125	1.00[CHD][hapmap]
rs11721286	0.91[EUR][1000 genomes]
rs123598	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs123603	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13060192	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]
rs13065677	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs13071708	1.00[ASW][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs13074649	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075370	1.00[CHD][hapmap]
rs13076508	0.95[AMR][1000 genomes]
rs13089892	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13091360	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13093555	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs13096571	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13098856	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs1541495	0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs164636	0.91[AMR][1000 genomes]
rs164637	0.91[AMR][1000 genomes]
rs17052068	1.00[CHD][hapmap]
rs2109557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2109558	1.00[ASW][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs2109559	1.00[ASW][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs2215466	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335640	1.00[CHD][hapmap]
rs2335928	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335929	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878549	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34181173	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34332947	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34385735	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs34551211	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs34628357	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34762015	1.00[CHD][hapmap]
rs34827613	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35130772	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs352141	0.82[AMR][1000 genomes]
rs352144	0.86[AMR][1000 genomes]
rs353545	0.91[AMR][1000 genomes]
rs35860312	1.00[CHD][hapmap]
rs35982798	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3774409	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796342	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs409803	0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs419050	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs419604	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs419752	1.00[ASW][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4312651	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687541	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687543	0.83[EUR][1000 genomes]
rs4687544	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687614	1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687616	0.88[EUR][1000 genomes]
rs4687617	1.00[ASW][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs4687618	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687619	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687621	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498778	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs575476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs613519	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61734640	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6414568	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445483	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445484	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445485	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445486	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445506	1.00[ASW][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs676034	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763882	1.00[CHD][hapmap]
rs6771558	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782162	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784615	1.00[ASW][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs6787493	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6795333	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6810027	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71297391	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs71297394	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs71297395	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs71297396	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs728408	1.00[ASW][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs758800	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs758803	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620015	1.00[ASW][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs887514	1.00[ASW][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs929528	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929529	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846089	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9847332	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850471	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855470	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863753	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9867823	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv876794	chr3:52485876-52496229	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52478800-52487600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr3:52479400-52487200	Weak transcription	GM12878-XiMat	blood
3	chr3:52479400-52488200	Weak transcription	Colonic Mucosa	Colon
4	chr3:52479600-52487400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr3:52479600-52487600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr3:52479600-52487600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:52479600-52487800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:52481200-52487600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:52481200-52490000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:52481400-52487400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr3:52481400-52488200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:52481600-52487200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr3:52483800-52489000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:52483800-52489200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:52484000-52488000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
16	chr3:52484200-52487800	Weak transcription	Spleen	Spleen
17	chr3:52484400-52487200	Weak transcription	Esophagus	oesophagus
18	chr3:52484600-52487200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:52484600-52487400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:52484600-52487600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:52484600-52487800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:52484600-52487800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:52484600-52488400	Weak transcription	NHEK	skin
24	chr3:52484600-52488800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:52484600-52489200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:52484800-52487600	Weak transcription	Lung	lung
27	chr3:52484800-52489000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:52484800-52489000	Weak transcription	NH-A	brain
29	chr3:52485000-52488000	Active TSS	Right Atrium	heart
30	chr3:52485000-52488200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:52485000-52488600	Weak transcription	Liver	Liver
32	chr3:52485000-52488600	Weak transcription	HMEC	breast
33	chr3:52485200-52489200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:52485400-52489000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:52485600-52487600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:52485600-52489400	Flanking Active TSS	HepG2	liver
37	chr3:52486200-52487200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:52486200-52487200	Enhancers	Fetal Muscle Leg	muscle
39	chr3:52486200-52487400	Weak transcription	Placenta	Placenta
40	chr3:52486200-52487600	Active TSS	Fetal Heart	heart
41	chr3:52486200-52487800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:52486200-52488600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:52486200-52489200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:52486400-52487200	Weak transcription	Psoas Muscle	Psoas
45	chr3:52486400-52487200	Enhancers	Stomach Mucosa	stomach
46	chr3:52486400-52488200	Active TSS	Right Ventricle	heart
47	chr3:52486400-52488400	Active TSS	Left Ventricle	heart
48	chr3:52486400-52488800	Weak transcription	Fetal Brain Female	brain
49	chr3:52486600-52487200	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr3:52486600-52487400	Enhancers	Hela-S3	cervix

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