Variant report

Variant	rs62410374
Chromosome Location	chr3:178978718-178978719
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	ELF1	chr3:178978703-178979434	MCF-7	breast:	n/a	chr3:178979336-178979345 chr3:178979261-178979273 chr3:178979004-178979017 chr3:178979196-178979205
2	TBP	chr3:178978627-178979468	K562	blood:	n/a	n/a
3	MAX	chr3:178978679-178979810	ECC-1	luminal epithelium:	n/a	chr3:178979295-178979305
4	JUND	chr3:178978622-178979591	K562	blood:	n/a	chr3:178979356-178979365
5	MAX	chr3:178978625-178979566	HepG2	liver:	n/a	chr3:178979295-178979305
6	E2F6	chr3:178978715-178979467	H1-hESC	embryonic stem cell:	n/a	chr3:178979088-178979097 chr3:178979089-178979096 chr3:178979089-178979096 chr3:178979089-178979096
7	POLR2A	chr3:178978713-178979431	MCF-7	breast:	n/a	n/a
8	MAX	chr3:178978552-178979560	A549	lung:	n/a	chr3:178979295-178979305
9	MAX	chr3:178978656-178979495	A549	lung:	n/a	chr3:178979295-178979305
10	HA-E2F1	chr3:178978522-178979654	MCF-7	breast:	n/a	chr3:178979088-178979097 chr3:178979089-178979096 chr3:178979089-178979096 chr3:178979089-178979096
11	MYC	chr3:178978605-178979527	K562	blood:	n/a	chr3:178979295-178979305
12	E2F6	chr3:178978580-178979371	K562	blood:	n/a	chr3:178979088-178979097 chr3:178979089-178979096 chr3:178979089-178979096 chr3:178979089-178979096
13	POLR2A	chr3:178978669-178979536	K562	blood:	n/a	n/a
14	MAX	chr3:178978680-178979365	K562	blood:	n/a	chr3:178979295-178979305
15	UBTF	chr3:178978605-178979515	K562	blood:	n/a	n/a
16	E2F6	chr3:178978388-178979369	H1-hESC	embryonic stem cell:	n/a	chr3:178979088-178979097 chr3:178979089-178979096 chr3:178979089-178979096 chr3:178979089-178979096
17	MAX	chr3:178978371-178979455	K562	blood:	n/a	chr3:178979295-178979305
18	CCNT2	chr3:178978613-178979465	K562	blood:	n/a	chr3:178979263-178979272
19	HCFC1	chr3:178978484-178979457	K562	blood:	n/a	n/a
20	MAX	chr3:178978714-178979492	H1-hESC	embryonic stem cell:	n/a	chr3:178979295-178979305
21	MAZ	chr3:178978470-178979536	K562	blood:	n/a	chr3:178979295-178979305
22	RCOR1	chr3:178978417-178979254	K562	blood:	n/a	n/a
23	ELF1	chr3:178978651-178979430	K562	blood:	n/a	chr3:178979336-178979345 chr3:178979261-178979273 chr3:178979004-178979017 chr3:178979196-178979205
24	MAZ	chr3:178978660-178979677	IMR90	lung:	n/a	chr3:178979295-178979305
25	MAX	chr3:178978651-178979547	ECC-1	luminal epithelium:	n/a	chr3:178979295-178979305
26	POLR2A	chr3:178976734-178979717	K562	blood:	n/a	n/a
27	SETDB1	chr3:178978302-178979469	K562	blood:	n/a	n/a
28	YY1	chr3:178978686-178978869	K562	blood:	n/a	n/a
29	POLR2A	chr3:178978651-178979398	K562	blood:	n/a	n/a
30	BHLHE40	chr3:178978584-178978761	GM12878	blood:	n/a	n/a
31	ELF1	chr3:178978674-178979464	GM12878	blood:	n/a	chr3:178979336-178979345 chr3:178979261-178979273 chr3:178979004-178979017 chr3:178979196-178979205
32	SPI1	chr3:178978675-178978933	K562	blood:	n/a	n/a
33	SPI1	chr3:178978635-178978940	GM12878	blood:	n/a	n/a
34	MYC	chr3:178978627-178979671	K562	blood:	n/a	chr3:178979295-178979305
35	POLR2A	chr3:178978697-178979481	GM18505	blood:	n/a	n/a
36	POLR2A	chr3:178978665-178979360	HepG2	liver:	n/a	n/a
37	POLR2A	chr3:178977724-178979470	K562	blood:	n/a	n/a
38	MAX	chr3:178978642-178979499	K562	blood:	n/a	chr3:178979295-178979305
39	POLR2A	chr3:178976506-178979311	K562	blood:	n/a	n/a
40	MAX	chr3:178978587-178979507	MCF-7	breast:	n/a	chr3:178979295-178979305
41	POLR2A	chr3:178978655-178979416	HepG2	liver:	n/a	n/a
42	E2F6	chr3:178977678-178979605	K562	blood:	n/a	chr3:178979088-178979097 chr3:178979089-178979096 chr3:178979089-178979096 chr3:178979089-178979096
43	SETDB1	chr3:178976585-178979817	U2OS	brain:	n/a	n/a
44	E2F6	chr3:178978697-178979318	A549	lung:	n/a	chr3:178979088-178979097 chr3:178979089-178979096 chr3:178979089-178979096 chr3:178979089-178979096
45	TBL1XR1	chr3:178978484-178978765	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:178978446..178980464-chr3:179279567..179281993,2	K562	blood:
2	chr3:178866930..178870480-chr3:178976906..178979282,3	K562	blood:
3	chr3:178971723..178977145-chr3:178977567..178980865,6	K562	blood:
4	chr3:178863877..178868371-chr3:178977065..178980370,6	K562	blood:
5	chr3:178976479..178980556-chr3:178981755..178985679,10	K562	blood:
6	chr3:178787758..178789707-chr3:178977770..178980269,2	MCF-7	breast:
7	chr3:178863877..178866682-chr3:178977686..178979355,3	K562	blood:
8	chr3:178977431..178979193-chr3:179039095..179041437,2	MCF-7	breast:
9	chr3:178976102..178980828-chr3:178981002..178985885,12	K562	blood:
10	chr3:178865885..178868102-chr3:178977747..178979601,3	MCF-7	breast:
11	chr3:178977854..178979821-chr3:179040251..179043018,2	MCF-7	breast:
12	chr3:178978041..178980864-chr3:179039699..179042008,3	K562	blood:
13	chr3:178977469..178980839-chr3:179038593..179042214,6	K562	blood:

Variant related genes	Relation type
KCNMB3	TF binding region
ENSG00000121864	Chromatin interaction
ENSG00000136518	Chromatin interaction
ENSG00000172667	Chromatin interaction
ENSG00000171121	Chromatin interaction
ENSG00000229102	Chromatin interaction
ENSG00000121879	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10804876	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804877	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10804878	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10804879	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10936995	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720871	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720935	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12631127	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12633678	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12633724	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1477190	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1968207	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1968208	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2864412	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56295844	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56400023	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410370	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410371	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773405	0.99[AFR][1000 genomes];0.99[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];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639338	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7642066	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178949000-178978800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:178959800-178978800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:178963200-178978800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:178963800-178978800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:178972000-178978800	Weak transcription	Small Intestine	intestine
6	chr3:178975800-178978800	Weak transcription	Gastric	stomach
7	chr3:178977400-178978800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:178977600-178978800	Flanking Active TSS	K562	blood
9	chr3:178977600-178979000	Flanking Active TSS	GM12878-XiMat	blood
10	chr3:178977800-178978800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
11	chr3:178977800-178978800	Weak transcription	Fetal Thymus	thymus
12	chr3:178978000-178978800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:178978200-178979600	Active TSS	Colon Smooth Muscle	Colon
14	chr3:178978200-178979800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:178978400-178978800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:178978400-178978800	Enhancers	Primary B cells from peripheral blood	blood
17	chr3:178978400-178978800	Enhancers	Primary T cells fromperipheralblood	blood
18	chr3:178978400-178978800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:178978400-178978800	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr3:178978400-178978800	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr3:178978400-178978800	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr3:178978400-178978800	Flanking Active TSS	Rectal Smooth Muscle	rectum
23	chr3:178978400-178978800	Flanking Active TSS	HepG2	liver
24	chr3:178978400-178979000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:178978400-178979000	ZNF genes & repeats	Fetal Intestine Small	intestine
26	chr3:178978400-178979400	Active TSS	Brain Anterior Caudate	brain
27	chr3:178978400-178979600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
28	chr3:178978400-178979600	Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr3:178978400-178979800	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr3:178978400-178979800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:178978400-178979800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:178978400-178979800	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr3:178978400-178979800	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr3:178978400-178979800	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr3:178978400-178980000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:178978600-178978800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:178978600-178978800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
38	chr3:178978600-178978800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:178978600-178978800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
40	chr3:178978600-178978800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr3:178978600-178978800	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr3:178978600-178978800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:178978600-178978800	Flanking Active TSS	Brain Cingulate Gyrus	brain
44	chr3:178978600-178978800	ZNF genes & repeats	Fetal Muscle Leg	muscle
45	chr3:178978600-178978800	Flanking Active TSS	Pancreas	Pancrea
46	chr3:178978600-178978800	Flanking Active TSS	NHEK	skin
47	chr3:178978600-178978800	Flanking Active TSS	Osteobl	bone
48	chr3:178978600-178979000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr3:178978600-178979000	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr3:178978600-178979000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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