Variant report

Variant	rs10027564
Chromosome Location	chr4:69185291-69185292
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	POLR2A	chr4:69185235-69185311	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr4:69184146-69185869	K562	blood:	n/a	n/a
3	POLR2A	chr4:69184205-69185899	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
YTHDC1	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10024896	1.00[EUR][1000 genomes]
rs10031034	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11932381	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11940780	1.00[EUR][1000 genomes]
rs11942378	1.00[EUR][1000 genomes]
rs17089253	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2056802	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2319796	1.00[TSI][hapmap]
rs28633232	1.00[EUR][1000 genomes]
rs28758556	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28866177	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35883654	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7664735	1.00[EUR][1000 genomes]
rs7684922	1.00[EUR][1000 genomes]
rs9994462	1.00[TSI][hapmap]
rs9998289	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008084	chr4:68797598-69482831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv537131	chr4:68797598-69482831	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1806586	chr4:68943858-69592846	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv461546	chr4:69049643-69223057	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv594506	chr4:69049643-69223057	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv537132	chr4:69149648-69482831	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh 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	22 gene(s)	inside rSNPs	diseases
7	esv2757061	chr4:69178920-69631668	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers 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	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69176200-69203600	Strong transcription	Liver	Liver
2	chr4:69176200-69203600	Strong transcription	HSMM	muscle
3	chr4:69176200-69204000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:69176200-69204200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:69176400-69185400	Strong transcription	Brain Germinal Matrix	brain
6	chr4:69176400-69185400	Strong transcription	Fetal Muscle Trunk	muscle
7	chr4:69176400-69185600	Strong transcription	Brain Anterior Caudate	brain
8	chr4:69176400-69186000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:69176400-69186000	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr4:69176400-69186000	Strong transcription	Adipose Nuclei	Adipose
11	chr4:69176400-69186200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:69176400-69188800	Strong transcription	GM12878-XiMat	blood
13	chr4:69176400-69203800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:69176400-69204000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:69176400-69204400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:69176400-69204600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:69176600-69185400	Strong transcription	Primary T cells from cord blood	blood
18	chr4:69176600-69185800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr4:69176600-69190200	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr4:69176600-69198400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:69176600-69203600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:69176600-69204600	Strong transcription	Fetal Thymus	thymus
23	chr4:69176800-69185400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr4:69176800-69202200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr4:69176800-69203600	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr4:69177200-69203600	Strong transcription	Placenta	Placenta
27	chr4:69177200-69203800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:69177200-69204200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:69177400-69190000	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr4:69177400-69204000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr4:69177600-69186000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr4:69177800-69185600	Strong transcription	HMEC	breast
33	chr4:69177800-69186000	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr4:69177800-69201200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr4:69177800-69203800	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr4:69178000-69185800	Strong transcription	Colon Smooth Muscle	Colon
37	chr4:69178000-69185800	Strong transcription	Fetal Kidney	kidney
38	chr4:69178000-69186000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr4:69178000-69186200	Strong transcription	Osteobl	bone
40	chr4:69178000-69190600	Strong transcription	HUVEC	blood vessel
41	chr4:69178000-69203600	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr4:69178000-69205000	Strong transcription	Dnd41	blood
43	chr4:69178200-69188000	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr4:69178200-69189600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:69178200-69193200	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr4:69178400-69187600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr4:69178800-69185400	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr4:69179000-69186200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr4:69179200-69194200	Weak transcription	Hela-S3	cervix
50	chr4:69179200-69198600	Strong transcription	NHEK	skin

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