Variant report

Variant	rs74125065
Chromosome Location	chr1:151034535-151034536
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	REST	chr1:151031025-151034997	H1-neurons	neurons:	n/a	chr1:151031403-151031416 chr1:151032692-151032702 chr1:151032963-151032976
2	CHD1	chr1:151029888-151034886	IMR90	lung:	n/a	n/a
3	MXI1	chr1:151029883-151034838	SK-N-SH	brain:	n/a	n/a
4	EP300	chr1:151029972-151034687	SK-N-SH	brain:	n/a	chr1:151031911-151031920 chr1:151031778-151031794 chr1:151031908-151031924 chr1:151030872-151030881 chr1:151030649-151030663 chr1:151033804-151033811 chr1:151031736-151031750 chr1:151030871-151030885 chr1:151030308-151030322

No.	Distal block	Cell Line	Cell type
1	chr1:151032560..151034898-chr1:151112557..151115397,2	MCF-7	breast:
2	chr1:151032375..151034566-chr1:151127124..151130341,3	K562	blood:
3	chr1:150941235..150942777-chr1:151033520..151036344,2	K562	blood:
4	chr1:150967045..150969733-chr1:151032331..151034733,2	K562	blood:
5	chr1:151032215..151035377-chr20:48807213..48809551,3	MCF-7	breast:
6	chr1:150976723..150987587-chr1:151024685..151036322,24	MCF-7	breast:
7	chr1:151034097..151036685-chr20:45986006..45988926,2	MCF-7	breast:
8	chr1:150996357..150999455-chr1:151032530..151036839,3	K562	blood:

Variant related genes	Relation type
CDC42SE1	TF binding region
ENSG00000143418	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000172216	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000163154	Chromatin interaction
ENSG00000143409	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs41266626	0.83[EUR][1000 genomes]
rs41266630	1.00[EUR][1000 genomes]
rs41267548	1.00[EUR][1000 genomes]
rs41299635	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41310891	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41310905	1.00[EUR][1000 genomes]
rs55716130	1.00[AMR][1000 genomes]
rs55935377	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57330524	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58618837	1.00[AMR][1000 genomes]
rs58763463	1.00[AMR][1000 genomes]
rs59737164	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60636837	1.00[AMR][1000 genomes]
rs60865304	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74125051	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74125053	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74125059	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74125062	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74125063	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74125077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74125079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74125080	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74125087	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74125088	1.00[AMR][1000 genomes]
rs74125093	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74127505	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74127506	1.00[AMR][1000 genomes]
rs74127513	1.00[AMR][1000 genomes]
rs74127514	1.00[AMR][1000 genomes]
rs74127515	1.00[AMR][1000 genomes]
rs74127528	1.00[AMR][1000 genomes]
rs74127529	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74127530	1.00[AMR][1000 genomes]
rs74127531	1.00[AMR][1000 genomes]
rs74127535	1.00[AMR][1000 genomes]
rs74127536	1.00[AMR][1000 genomes]
rs74127539	1.00[AMR][1000 genomes]
rs74127540	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151030200-151035600	Active TSS	HSMMtube	muscle
2	chr1:151030600-151034800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:151030600-151035200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:151030800-151034600	Active TSS	Thymus	Thymus
5	chr1:151030800-151034800	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr1:151030800-151035200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:151030800-151035400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr1:151030800-151035800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:151031000-151034600	Active TSS	Brain Anterior Caudate	brain
10	chr1:151031000-151034600	Active TSS	A549	lung
11	chr1:151031000-151035200	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr1:151031200-151034600	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr1:151031200-151034800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:151031200-151035800	Active TSS	Brain Cingulate Gyrus	brain
15	chr1:151031400-151034800	Active TSS	Fetal Brain Male	brain
16	chr1:151031400-151035600	Active TSS	Brain Angular Gyrus	brain
17	chr1:151031400-151035800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:151031600-151035200	Active TSS	Fetal Brain Female	brain
19	chr1:151031600-151035600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:151031600-151035600	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr1:151031800-151034600	Active TSS	Muscle Satellite Cultured Cells	--
22	chr1:151031800-151035200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:151032200-151034600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr1:151032800-151034800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:151032800-151035200	Active TSS	NH-A	brain
26	chr1:151033000-151042800	Weak transcription	Gastric	stomach
27	chr1:151033200-151034800	Enhancers	Liver	Liver
28	chr1:151033200-151035200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:151033200-151042200	Weak transcription	Esophagus	oesophagus
30	chr1:151033200-151042200	Weak transcription	Pancreas	Pancrea
31	chr1:151033200-151042600	Weak transcription	Aorta	Aorta
32	chr1:151033400-151034600	Flanking Active TSS	Osteobl	bone
33	chr1:151033400-151034800	Flanking Active TSS	HUVEC	blood vessel
34	chr1:151033600-151034600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr1:151033600-151034600	Active TSS	Brain Hippocampus Middle	brain
36	chr1:151033600-151041800	Weak transcription	Primary B cells from cord blood	blood
37	chr1:151033600-151042200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:151033800-151034600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:151033800-151034600	Active TSS	Fetal Kidney	kidney
40	chr1:151033800-151035200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr1:151033800-151036400	Enhancers	Placenta Amnion	Placenta Amnion
42	chr1:151033800-151036600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:151033800-151038400	Weak transcription	Primary T cells from cord blood	blood
44	chr1:151033800-151042600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:151033800-151042600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr1:151033800-151042600	Weak transcription	Right Atrium	heart
47	chr1:151034000-151034600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:151034000-151035000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:151034000-151035800	Enhancers	Fetal Heart	heart
50	chr1:151034000-151036600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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