Variant report

Variant	rs62410371
Chromosome Location	chr3:178978328-178978329
allele	C/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	POLR2A	chr3:178977549-178978406	GM12892	blood:	n/a	n/a
2	CEBPB	chr3:178977748-178978451	K562	blood:	n/a	chr3:178978270-178978281
3	CEBPB	chr3:178978117-178978469	HepG2	liver:	n/a	chr3:178978270-178978281
4	HEY1	chr3:178977793-178978395	K562	blood:	n/a	n/a
5	CEBPB	chr3:178978195-178978464	A549	lung:	n/a	chr3:178978270-178978281
6	POLR2A	chr3:178977655-178978506	GM12892	blood:	n/a	n/a
7	BACH1	chr3:178977747-178978398	K562	blood:	n/a	n/a
8	CEBPB	chr3:178977750-178978649	K562	blood:	n/a	chr3:178978270-178978281
9	POLR2A	chr3:178976734-178979717	K562	blood:	n/a	n/a
10	SETDB1	chr3:178978302-178979469	K562	blood:	n/a	n/a
11	TRIM28	chr3:178977726-178978526	K562	blood:	n/a	n/a
12	CEBPB	chr3:178978151-178978413	IMR90	lung:	n/a	chr3:178978270-178978281
13	POLR2A	chr3:178977724-178979470	K562	blood:	n/a	n/a
14	POLR2A	chr3:178976506-178979311	K562	blood:	n/a	n/a
15	E2F6	chr3:178977678-178979605	K562	blood:	n/a	chr3:178979088-178979097 chr3:178979089-178979096 chr3:178979089-178979096 chr3:178979089-178979096
16	SETDB1	chr3:178976585-178979817	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:178866930..178870480-chr3:178976906..178979282,3	K562	blood:
2	chr3:178971723..178977145-chr3:178977567..178980865,6	K562	blood:
3	chr3:178863877..178868371-chr3:178977065..178980370,6	K562	blood:
4	chr3:178976479..178980556-chr3:178981755..178985679,10	K562	blood:
5	chr3:178787758..178789707-chr3:178977770..178980269,2	MCF-7	breast:
6	chr3:178863877..178866682-chr3:178977686..178979355,3	K562	blood:
7	chr3:178977431..178979193-chr3:179039095..179041437,2	MCF-7	breast:
8	chr3:178976102..178980828-chr3:178981002..178985885,12	K562	blood:
9	chr3:178865885..178868102-chr3:178977747..178979601,3	MCF-7	breast:
10	chr3:178977854..178979821-chr3:179040251..179043018,2	MCF-7	breast:
11	chr3:178978041..178980864-chr3:179039699..179042008,3	K562	blood:
12	chr3:178977469..178980839-chr3:179038593..179042214,6	K562	blood:

Variant related genes	Relation type
KCNMB3	TF binding region
ENSG00000121864	Chromatin interaction
ENSG00000172667	Chromatin interaction
ENSG00000229102	Chromatin interaction
ENSG00000121879	Chromatin interaction
ENSG00000171121	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10804876	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804877	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10804878	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10804879	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10936995	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720871	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720935	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12631127	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12633678	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12633724	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1477190	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1968207	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1968208	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2864412	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56295844	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56400023	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410372	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410373	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410374	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773405	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7429685	1.00[ASN][1000 genomes]
rs7617552	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639338	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7642066	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1010137	chr3:178962897-179050787	Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
10	nsv471116	chr3:178968634-179252263	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv592650	chr3:178968634-179252263	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers 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	35 gene(s)	inside rSNPs	diseases
12	nsv1010513	chr3:178976107-179196274	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv536816	chr3:178976107-179196274	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
14	nsv967094	chr3:178976467-178978666	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
15	nsv1014953	chr3:178977844-179006633	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178912400-178978600	Weak transcription	Right Ventricle	heart
2	chr3:178945800-178978400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:178948800-178978600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:178949000-178978600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:178949000-178978600	Weak transcription	Ovary	ovary
6	chr3:178949000-178978800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:178949200-178978400	Weak transcription	Brain Anterior Caudate	brain
8	chr3:178949200-178978600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:178949200-178978600	Weak transcription	Osteobl	bone
10	chr3:178952000-178978400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:178952400-178978600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:178959800-178978800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:178963200-178978600	Weak transcription	Left Ventricle	heart
14	chr3:178963200-178978800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:178963800-178978800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:178966200-178978600	Weak transcription	HUVEC	blood vessel
17	chr3:178968800-178978400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:178968800-178978600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:178969200-178978400	Weak transcription	Primary B cells from cord blood	blood
20	chr3:178969600-178978600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:178972000-178978800	Weak transcription	Small Intestine	intestine
22	chr3:178975000-178978400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:178975800-178978800	Weak transcription	Gastric	stomach
24	chr3:178976800-178978400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:178976800-178978400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:178977400-178978600	Weak transcription	Brain Angular Gyrus	brain
27	chr3:178977400-178978800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:178977600-178978800	Flanking Active TSS	K562	blood
29	chr3:178977600-178979000	Flanking Active TSS	GM12878-XiMat	blood
30	chr3:178977800-178978600	Enhancers	Pancreas	Pancrea
31	chr3:178977800-178978800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
32	chr3:178977800-178978800	Weak transcription	Fetal Thymus	thymus
33	chr3:178978000-178978400	Enhancers	HepG2	liver
34	chr3:178978000-178978800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:178978200-178978400	Active TSS	Rectal Smooth Muscle	rectum
36	chr3:178978200-178978600	Active TSS	Muscle Satellite Cultured Cells	--
37	chr3:178978200-178978600	Enhancers	Hela-S3	cervix
38	chr3:178978200-178978600	Active TSS	NHLF	lung
39	chr3:178978200-178979600	Active TSS	Colon Smooth Muscle	Colon
40	chr3:178978200-178979800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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