Variant report

Variant	rs62410372
Chromosome Location	chr3:178978542-178978543
allele	A/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	IRF1	chr3:178978390-178978684	K562	blood:	n/a	n/a
2	HA-E2F1	chr3:178978522-178979654	MCF-7	breast:	n/a	chr3:178979088-178979097 chr3:178979089-178979096 chr3:178979089-178979096 chr3:178979089-178979096
3	E2F6	chr3:178978388-178979369	H1-hESC	embryonic stem cell:	n/a	chr3:178979088-178979097 chr3:178979089-178979096 chr3:178979089-178979096 chr3:178979089-178979096
4	MAX	chr3:178978371-178979455	K562	blood:	n/a	chr3:178979295-178979305
5	CEBPB	chr3:178977750-178978649	K562	blood:	n/a	chr3:178978270-178978281
6	HCFC1	chr3:178978484-178979457	K562	blood:	n/a	n/a
7	MAZ	chr3:178978470-178979536	K562	blood:	n/a	chr3:178979295-178979305
8	RCOR1	chr3:178978417-178979254	K562	blood:	n/a	n/a
9	POLR2A	chr3:178976734-178979717	K562	blood:	n/a	n/a
10	SETDB1	chr3:178978302-178979469	K562	blood:	n/a	n/a
11	POLR2A	chr3:178977724-178979470	K562	blood:	n/a	n/a
12	POLR2A	chr3:178976506-178979311	K562	blood:	n/a	n/a
13	E2F6	chr3:178977678-178979605	K562	blood:	n/a	chr3:178979088-178979097 chr3:178979089-178979096 chr3:178979089-178979096 chr3:178979089-178979096
14	SETDB1	chr3:178976585-178979817	U2OS	brain:	n/a	n/a
15	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
ENSG00000121879	Chromatin interaction
ENSG00000229102	Chromatin interaction
ENSG00000172667	Chromatin interaction
ENSG00000121864	Chromatin interaction
ENSG00000136518	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];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]
rs62410373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410374	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: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:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178912400-178978600	Weak transcription	Right Ventricle	heart
2	chr3:178948800-178978600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:178949000-178978600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:178949000-178978600	Weak transcription	Ovary	ovary
5	chr3:178949000-178978800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:178949200-178978600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:178949200-178978600	Weak transcription	Osteobl	bone
8	chr3:178952400-178978600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:178959800-178978800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:178963200-178978600	Weak transcription	Left Ventricle	heart
11	chr3:178963200-178978800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:178963800-178978800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:178966200-178978600	Weak transcription	HUVEC	blood vessel
14	chr3:178968800-178978600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:178969600-178978600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:178972000-178978800	Weak transcription	Small Intestine	intestine
17	chr3:178975800-178978800	Weak transcription	Gastric	stomach
18	chr3:178977400-178978600	Weak transcription	Brain Angular Gyrus	brain
19	chr3:178977400-178978800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:178977600-178978800	Flanking Active TSS	K562	blood
21	chr3:178977600-178979000	Flanking Active TSS	GM12878-XiMat	blood
22	chr3:178977800-178978600	Enhancers	Pancreas	Pancrea
23	chr3:178977800-178978800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
24	chr3:178977800-178978800	Weak transcription	Fetal Thymus	thymus
25	chr3:178978000-178978800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:178978200-178978600	Active TSS	Muscle Satellite Cultured Cells	--
27	chr3:178978200-178978600	Enhancers	Hela-S3	cervix
28	chr3:178978200-178978600	Active TSS	NHLF	lung
29	chr3:178978200-178979600	Active TSS	Colon Smooth Muscle	Colon
30	chr3:178978200-178979800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:178978400-178978600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:178978400-178978600	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr3:178978400-178978600	Enhancers	Primary B cells from cord blood	blood
34	chr3:178978400-178978600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:178978400-178978600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
36	chr3:178978400-178978600	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr3:178978400-178978600	Flanking Active TSS	Liver	Liver
38	chr3:178978400-178978600	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr3:178978400-178978600	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr3:178978400-178978600	ZNF genes & repeats	A549	lung
41	chr3:178978400-178978600	Active TSS	Monocytes-CD14+_RO01746	blood
42	chr3:178978400-178978600	ZNF genes & repeats	NHEK	skin
43	chr3:178978400-178978800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:178978400-178978800	Enhancers	Primary B cells from peripheral blood	blood
45	chr3:178978400-178978800	Enhancers	Primary T cells fromperipheralblood	blood
46	chr3:178978400-178978800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:178978400-178978800	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr3:178978400-178978800	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr3:178978400-178978800	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr3:178978400-178978800	Flanking Active TSS	Rectal Smooth Muscle	rectum

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