Variant report

Variant	rs6925652
Chromosome Location	chr6:56112781-56112782
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	MAX	chr6:56111599-56112855	H1-hESC	embryonic stem cell:	n/a	chr6:56111822-56111831
2	KAP1	chr6:56111703-56113202	HEK293	kidney:	n/a	n/a
3	CTBP2	chr6:56111522-56112844	H1-hESC	embryonic stem cell:	n/a	n/a
4	SIN3A	chr6:56111385-56112910	H1-hESC	embryonic stem cell:	n/a	chr6:56112015-56112026 chr6:56111811-56111824 chr6:56112806-56112814

Variant related genes	Relation type
COL21A1	TF binding region

Extended variants
information (count: 5 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10223442	1.00[CHB][hapmap]
rs6903416	1.00[CHB][hapmap];0.90[GIH][hapmap]
rs6919257	0.81[TSI][hapmap]
rs9296834	1.00[CHB][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885911	chr6:55789704-56143231	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6925652	GCM1	cis	cerebellum	SCAN
rs6925652	COL21A1	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56109400-56113000	Active TSS	Aorta	Aorta
2	chr6:56110400-56112800	Active TSS	Fetal Kidney	kidney
3	chr6:56111400-56112800	Active TSS	Brain Angular Gyrus	brain
4	chr6:56111400-56112800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
5	chr6:56111400-56112800	Active TSS	Brain Substantia Nigra	brain
6	chr6:56111400-56112800	Active TSS	Colon Smooth Muscle	Colon
7	chr6:56111400-56112800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
8	chr6:56111400-56112800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr6:56111400-56112800	Active TSS	NHLF	lung
10	chr6:56111400-56113000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:56111400-56113000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:56111400-56113000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:56111600-56112800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:56111600-56112800	Active TSS	Brain Anterior Caudate	brain
15	chr6:56111600-56112800	Active TSS	Left Ventricle	heart
16	chr6:56111600-56112800	Flanking Active TSS	NHEK	skin
17	chr6:56111600-56113000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:56111600-56113000	Flanking Active TSS	Osteobl	bone
19	chr6:56111800-56112800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:56111800-56112800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr6:56111800-56112800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:56111800-56112800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:56111800-56112800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
24	chr6:56111800-56112800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
25	chr6:56111800-56112800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
26	chr6:56111800-56112800	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
27	chr6:56111800-56112800	Active TSS	Right Atrium	heart
28	chr6:56111800-56113000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:56112000-56112800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:56112000-56112800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:56112000-56112800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
32	chr6:56112000-56112800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
33	chr6:56112000-56112800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
34	chr6:56112000-56112800	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr6:56112000-56112800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
36	chr6:56112000-56112800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr6:56112000-56112800	Bivalent Enhancer	Stomach Mucosa	stomach
38	chr6:56112200-56112800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:56112200-56112800	Bivalent/Poised TSS	Fetal Brain Female	brain
40	chr6:56112200-56112800	Bivalent/Poised TSS	HUVEC	blood vessel
41	chr6:56112400-56112800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:56112400-56112800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:56112400-56112800	Flanking Active TSS	Fetal Muscle Trunk	muscle
44	chr6:56112400-56112800	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr6:56112400-56112800	Enhancers	Gastric	stomach
46	chr6:56112400-56113000	Flanking Active TSS	Fetal Lung	lung
47	chr6:56112400-56113400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr6:56112600-56112800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
49	chr6:56112600-56112800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr6:56112600-56112800	Flanking Active TSS	H1 Cell Line	embryonic stem cell

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