Variant report

Variant	rs549564
Chromosome Location	chr4:56286717-56286718
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	POLR2A	chr4:56286351-56286809	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr4:56286417-56287055	K562	blood:	n/a	n/a
3	POLR2A	chr4:56286500-56286747	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr4:56286635-56286758	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:56280205..56283146-chr4:56283949..56286738,4	K562	blood:
2	chr4:56285803..56288073-chr4:56308391..56310039,2	K562	blood:
3	chr4:56275809..56278262-chr4:56283958..56286779,2	K562	blood:
4	chr4:56284331..56287070-chr4:56288996..56292561,4	K562	blood:

Variant related genes	Relation type
TMEM165	TF binding region
ENSG00000134851	Chromatin interaction
ENSG00000134852	Chromatin interaction
ENSG00000203615	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11133399	0.85[YRI][hapmap]
rs11721546	0.88[ASN][1000 genomes]
rs11724565	0.88[ASN][1000 genomes]
rs11727586	0.86[EUR][1000 genomes]
rs11733128	0.88[ASN][1000 genomes]
rs1873092	0.85[YRI][hapmap]
rs2459220	0.89[ASN][1000 genomes]
rs471546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480531	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4864984	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491381	1.00[CHB][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505861	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530875	0.95[EUR][1000 genomes]
rs532768	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566240	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554276	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66630638	0.88[ASN][1000 genomes]
rs6837710	0.85[YRI][hapmap]
rs711533	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs726967	0.85[YRI][hapmap]
rs73236137	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7663955	0.89[ASN][1000 genomes]
rs7664496	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7669259	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7672647	0.82[ASN][1000 genomes]
rs7673897	0.88[ASN][1000 genomes]
rs7692795	1.00[CHB][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7697835	0.88[ASN][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	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1011722	chr4:56261349-56325600	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 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	chr4:56264800-56292200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:56265600-56289800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:56265600-56319800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:56268800-56326000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:56269000-56311400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr4:56274600-56332200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:56275600-56292400	Weak transcription	Stomach Mucosa	stomach
8	chr4:56275800-56300000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:56275800-56302200	Strong transcription	Fetal Thymus	thymus
10	chr4:56276000-56302400	Strong transcription	Dnd41	blood
11	chr4:56276000-56320000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:56276200-56292400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:56276200-56296800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr4:56276200-56304400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:56276200-56310000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:56276400-56297800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr4:56276600-56296400	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr4:56276600-56303400	Strong transcription	Osteobl	bone
19	chr4:56276600-56305000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr4:56277000-56292600	Weak transcription	Fetal Heart	heart
21	chr4:56277000-56296800	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:56277400-56302400	Strong transcription	HSMM	muscle
23	chr4:56277400-56306000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:56277600-56287800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:56277600-56301800	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr4:56277600-56305000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:56277800-56290800	Strong transcription	Fetal Stomach	stomach
28	chr4:56277800-56293200	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr4:56277800-56302200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:56278200-56301000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:56279000-56290800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:56279000-56293000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr4:56279000-56294800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:56279000-56300200	Strong transcription	HUVEC	blood vessel
35	chr4:56279000-56321800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr4:56279200-56296200	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr4:56279400-56290800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:56279600-56291000	Strong transcription	Fetal Brain Female	brain
39	chr4:56280000-56304800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr4:56280200-56292000	Strong transcription	Fetal Intestine Large	intestine
41	chr4:56280200-56296400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:56280400-56301000	Strong transcription	GM12878-XiMat	blood
43	chr4:56280600-56287000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
44	chr4:56280600-56287000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:56280600-56287000	Strong transcription	NHLF	lung
46	chr4:56280600-56288400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr4:56280600-56291200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:56280600-56292600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr4:56280600-56294800	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr4:56280600-56296200	Strong transcription	Sigmoid Colon	Sigmoid Colon

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