Variant report

Variant	rs56382488
Chromosome Location	chr4:73963297-73963298
allele	G/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	chr4:73961988-73964457	K562	blood:	n/a	n/a
2	POLR2A	chr4:73963102-73963362	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:73961420..73964354-chr4:73975853..73978637,2	K562	blood:
2	chr4:73955525..73957115-chr4:73962530..73964538,2	K562	blood:
3	chr4:73946540..73955069-chr4:73955536..73964230,11	K562	blood:

Variant related genes	Relation type
HMGA1P2	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11933644	0.84[ASN][1000 genomes]
rs16849102	0.87[ASN][1000 genomes]
rs16849106	0.90[ASN][1000 genomes]
rs16849108	0.90[ASN][1000 genomes]
rs16849146	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16849150	0.93[ASN][1000 genomes]
rs16849151	0.93[ASN][1000 genomes]
rs16849172	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2061574	0.90[ASN][1000 genomes]
rs2061575	0.90[ASN][1000 genomes]
rs2061576	0.92[ASN][1000 genomes]
rs2061577	0.90[ASN][1000 genomes]
rs2306057	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2366716	0.87[ASN][1000 genomes]
rs28373296	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28460851	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28709646	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28776801	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3796680	0.91[ASN][1000 genomes]
rs4019514	0.87[ASN][1000 genomes]
rs4631009	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4694589	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56235322	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57330350	0.95[ASN][1000 genomes]
rs61149200	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61468561	0.87[ASN][1000 genomes]
rs61661011	0.84[ASN][1000 genomes]
rs6824334	0.81[ASN][1000 genomes]
rs6845845	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6849701	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6851670	0.90[ASN][1000 genomes]
rs72663032	0.85[ASN][1000 genomes]
rs72859248	0.87[ASN][1000 genomes]
rs72859249	0.87[ASN][1000 genomes]
rs72861861	0.81[EUR][1000 genomes]
rs7661799	0.81[EUR][1000 genomes]
rs7670286	0.87[ASN][1000 genomes]
rs7674847	0.87[ASN][1000 genomes]
rs7675007	0.88[ASN][1000 genomes]
rs7675027	0.88[ASN][1000 genomes]
rs7676278	0.87[ASN][1000 genomes]
rs7679277	0.84[ASN][1000 genomes]
rs7687433	0.87[ASN][1000 genomes]
rs7690799	0.87[ASN][1000 genomes]
rs7691344	0.87[ASN][1000 genomes]
rs7692749	0.87[ASN][1000 genomes]
rs7694505	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949371	chr4:73678470-74094500	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv432611	chr4:73740665-74099265	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv523169	chr4:73752242-74120910	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv998707	chr4:73753922-74044843	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv537136	chr4:73753922-74044843	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv917017	chr4:73754127-74044830	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv1013174	chr4:73785324-74031884	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv537137	chr4:73785324-74031884	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv1012068	chr4:73817769-74003079	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv1014088	chr4:73817769-74031884	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv537138	chr4:73817769-74031884	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv533502	chr4:73819067-74044813	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	esv1849323	chr4:73926670-74115116	Strong transcription Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:73936000-73969600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:73936200-73980000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:73936400-73970000	Weak transcription	Stomach Mucosa	stomach
4	chr4:73938800-74005200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:73939000-73969600	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr4:73939000-74005000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:73939400-73970000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:73940400-74043400	Strong transcription	Fetal Thymus	thymus
9	chr4:73946800-73968000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:73949200-73988200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:73950600-74004200	Strong transcription	HSMM	muscle
12	chr4:73952800-73992400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:73952800-74023000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:73953000-73969800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:73953600-73963400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:73954600-73968400	Strong transcription	Fetal Muscle Trunk	muscle
17	chr4:73954600-73992200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:73954600-73995400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:73955200-73972800	Strong transcription	Placenta	Placenta
20	chr4:73955200-73991400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:73955200-73991600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:73955400-73970400	Strong transcription	Dnd41	blood
23	chr4:73955600-73968200	Strong transcription	Osteobl	bone
24	chr4:73955800-73968600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:73955800-73969000	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr4:73955800-73969800	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr4:73955800-74019000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr4:73955800-74022400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr4:73956000-73995600	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr4:73956200-73968200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr4:73956200-73968200	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr4:73956200-73968200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:73956200-73968200	Strong transcription	Liver	Liver
34	chr4:73956200-73968200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr4:73956200-73968400	Strong transcription	Primary B cells from peripheral blood	blood
36	chr4:73956200-73968400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:73956200-73970200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr4:73956400-73968000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr4:73956400-73968000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:73956600-73968400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:73957000-73968400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr4:73957600-73973600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr4:73957600-73985200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr4:73957800-73963400	Weak transcription	Fetal Brain Male	brain
45	chr4:73957800-73963800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:73957800-73963800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr4:73957800-73963800	Weak transcription	Brain Angular Gyrus	brain
48	chr4:73957800-73963800	Weak transcription	Fetal Heart	heart
49	chr4:73957800-73964400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr4:73957800-73964400	Weak transcription	Gastric	stomach

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