Variant report

Variant	rs3906410
Chromosome Location	chr5:96517732-96517733
allele	C/G
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	JUN	chr5:96517367-96517922	Hela-S3	cervix:	n/a	chr5:96517733-96517742
2	FOS	chr5:96517532-96517920	MCF10A-Er-Src	breast:	n/a	chr5:96517733-96517742
3	JUND	chr5:96517672-96517879	HepG2	liver:	n/a	chr5:96517732-96517743 chr5:96517733-96517742
4	EP300	chr5:96517565-96517974	Hela-S3	cervix:	n/a	chr5:96517609-96517619
5	STAT3	chr5:96517681-96517881	MCF10A-Er-Src	breast:	n/a	chr5:96517763-96517771
6	POLR2A	chr5:96517510-96517913	MCF10A-Er-Src	breast:	n/a	n/a
7	JUND	chr5:96517596-96517931	K562	blood:	n/a	chr5:96517732-96517743 chr5:96517733-96517742
8	CEBPB	chr5:96517590-96517902	A549	lung:	n/a	chr5:96517763-96517774 chr5:96517763-96517772 chr5:96517755-96517766 chr5:96517753-96517764 chr5:96517761-96517774
9	CEBPB	chr5:96517549-96517950	K562	blood:	n/a	chr5:96517763-96517774 chr5:96517763-96517772 chr5:96517755-96517766 chr5:96517753-96517764 chr5:96517761-96517774
10	CEBPB	chr5:96517541-96517956	K562	blood:	n/a	chr5:96517763-96517774 chr5:96517763-96517772 chr5:96517755-96517766 chr5:96517753-96517764 chr5:96517761-96517774
11	MYC	chr5:96517513-96517803	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr5:96517173-96518467	MCF10A-Er-Src	breast:	n/a	chr5:96517304-96517314 chr5:96517304-96517314 chr5:96517733-96517742
13	MYC	chr5:96517678-96517877	MCF10A-Er-Src	breast:	n/a	n/a
14	IRF1	chr5:96517291-96517802	K562	blood:	n/a	n/a
15	CEBPB	chr5:96517571-96517950	IMR90	lung:	n/a	chr5:96517763-96517774 chr5:96517763-96517772 chr5:96517755-96517766 chr5:96517753-96517764 chr5:96517761-96517774
16	ARID3A	chr5:96517679-96517912	K562	blood:	n/a	n/a
17	FOS	chr5:96517562-96518034	MCF10A-Er-Src	breast:	n/a	chr5:96517733-96517742
18	EP300	chr5:96517680-96517922	K562	blood:	n/a	n/a
19	JUND	chr5:96517548-96517937	Hela-S3	cervix:	n/a	chr5:96517732-96517743 chr5:96517733-96517742
20	FOS	chr5:96517225-96517923	MCF10A-Er-Src	breast:	n/a	chr5:96517304-96517314 chr5:96517304-96517314 chr5:96517733-96517742
21	CEBPB	chr5:96517578-96517914	HepG2	liver:	n/a	chr5:96517763-96517774 chr5:96517763-96517772 chr5:96517755-96517766 chr5:96517753-96517764 chr5:96517761-96517774
22	CEBPB	chr5:96517512-96518143	Hela-S3	cervix:	n/a	chr5:96517763-96517774 chr5:96517763-96517772 chr5:96517755-96517766 chr5:96517753-96517764 chr5:96517761-96517774

No.	Distal block	Cell Line	Cell type
1	chr5:96508014..96513294-chr5:96513654..96520413,9	K562	blood:
2	chr5:96517103..96519459-chr5:98107837..98111064,3	MCF-7	breast:
3	chr5:96142348..96143873-chr5:96516638..96519268,2	K562	blood:
4	chr5:96142588..96144739-chr5:96517628..96519299,2	MCF-7	breast:
5	chr5:96517585..96519769-chr5:96537536..96540052,2	MCF-7	breast:
6	chr5:96142348..96145031-chr5:96516210..96518138,3	K562	blood:

Variant related genes	Relation type
ENSG00000251513	TF binding region
ENSG00000174136	Chromatin interaction
ENSG00000206698	Chromatin interaction
ENSG00000248758	Chromatin interaction
ENSG00000246763	Chromatin interaction
ENSG00000164307	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10072369	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12515176	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1363943	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2216709	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2544773	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316183	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316184	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316185	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs316186	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316191	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316192	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316193	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316194	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316196	0.87[AMR][1000 genomes]
rs316197	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs316200	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs316215	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35824066	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs43497	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72777622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv830412	chr5:96427305-96606619	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1019790	chr5:96471680-96980633	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv537812	chr5:96471680-96980633	ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv882391	chr5:96496189-96533469	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv882392	chr5:96496189-96546238	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv882393	chr5:96496189-96567950	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96494400-96518000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:96495200-96518000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:96495600-96517800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:96514600-96518000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:96514600-96518000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:96514600-96518400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:96514600-96518600	Weak transcription	Spleen	Spleen
8	chr5:96514800-96518000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:96514800-96518000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:96514800-96518000	Weak transcription	Esophagus	oesophagus
11	chr5:96514800-96518000	Weak transcription	Left Ventricle	heart
12	chr5:96514800-96518000	Weak transcription	Lung	lung
13	chr5:96516000-96517800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:96516000-96517800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr5:96516000-96517800	Enhancers	Liver	Liver
16	chr5:96516000-96517800	Enhancers	Colon Smooth Muscle	Colon
17	chr5:96516000-96518000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr5:96516000-96518000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr5:96516000-96518000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr5:96516000-96518000	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr5:96516200-96517800	Weak transcription	Primary B cells from cord blood	blood
22	chr5:96516200-96517800	Enhancers	Stomach Mucosa	stomach
23	chr5:96516200-96518000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr5:96516400-96517800	Weak transcription	Fetal Thymus	thymus
25	chr5:96516400-96518000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr5:96516400-96518000	Weak transcription	Placenta	Placenta
27	chr5:96516600-96517800	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr5:96516600-96517800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr5:96516600-96517800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr5:96516600-96518000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:96516600-96519600	Active TSS	GM12878-XiMat	blood
32	chr5:96516600-96520200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:96516800-96517800	Weak transcription	Fetal Muscle Leg	muscle
34	chr5:96517000-96517800	Enhancers	Fetal Intestine Large	intestine
35	chr5:96517000-96517800	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr5:96517000-96518000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:96517000-96518000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr5:96517000-96518000	Enhancers	Small Intestine	intestine
39	chr5:96517000-96518200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:96517000-96518200	Flanking Active TSS	NHEK	skin
41	chr5:96517000-96518400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr5:96517000-96518400	Flanking Active TSS	Osteobl	bone
43	chr5:96517200-96517800	Enhancers	Primary hematopoietic stem cells	blood
44	chr5:96517200-96517800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr5:96517200-96517800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr5:96517200-96517800	Enhancers	Fetal Heart	heart
47	chr5:96517200-96517800	Enhancers	Fetal Stomach	stomach
48	chr5:96517200-96517800	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr5:96517200-96517800	Active TSS	Stomach Smooth Muscle	stomach
50	chr5:96517200-96517800	Flanking Active TSS	Hela-S3	cervix

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