Variant report

Variant	rs960750
Chromosome Location	chr2:172379686-172379687
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172288399..172293582-chr2:172376630..172381034,10	K562	blood:
2	chr2:172379590..172381198-chr2:172382870..172385036,2	MCF-7	breast:
3	chr2:172344598..172348821-chr2:172376554..172380965,4	K562	blood:
4	chr2:172016800..172018820-chr2:172378965..172381042,2	K562	blood:
5	chr2:172288399..172297381-chr2:172370978..172381493,22	K562	blood:
6	chr2:172377500..172380432-chr2:172864656..172866178,2	K562	blood:

Variant related genes	Relation type
ENSG00000172878	Chromatin interaction
ENSG00000123600	Chromatin interaction
ENSG00000198586	Chromatin interaction
ENSG00000115840	Chromatin interaction
ENSG00000228507	Chromatin interaction
ENSG00000115827	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10199858	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2356782	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6706526	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6749185	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs868106	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs960748	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs960749	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers 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	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs960750	CYBRD1	cis	brain	BrainEAC
rs960750	CYBRD1	cis	Esophagus Muscularis	GTEx
rs960750	CYBRD1	cis	Adipose Subcutaneous	GTEx
rs960750	CYBRD1	cis	intralobular white matter	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172378200-172380800	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr2:172378200-172381200	Active TSS	Right Atrium	heart
3	chr2:172378400-172380000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:172378400-172380200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:172378400-172380400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr2:172378400-172380400	Active TSS	GM12878-XiMat	blood
7	chr2:172378400-172380400	Active TSS	Hela-S3	cervix
8	chr2:172378400-172380600	Active TSS	Thymus	Thymus
9	chr2:172378400-172380600	Flanking Bivalent TSS/Enh	Dnd41	blood
10	chr2:172378400-172380800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr2:172378400-172380800	Active TSS	Right Ventricle	heart
12	chr2:172378400-172381000	Active TSS	Ovary	ovary
13	chr2:172378400-172381000	Flanking Active TSS	HMEC	breast
14	chr2:172378600-172380000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:172378600-172380200	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr2:172378600-172380200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:172378600-172380400	Active TSS	H9 Cell Line	embryonic stem cell
18	chr2:172378600-172380400	Active TSS	Brain Hippocampus Middle	brain
19	chr2:172378600-172380400	Active TSS	Monocytes-CD14+_RO01746	blood
20	chr2:172378600-172380600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:172378600-172380600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:172378600-172380600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:172378600-172380600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:172378600-172380600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:172378600-172380600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:172378600-172380600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:172378600-172380600	Active TSS	Brain Angular Gyrus	brain
28	chr2:172378600-172380600	Active TSS	Brain Anterior Caudate	brain
29	chr2:172378600-172380600	Active TSS	Brain Cingulate Gyrus	brain
30	chr2:172378600-172380600	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr2:172378600-172380600	Active TSS	Brain Substantia Nigra	brain
32	chr2:172378600-172380600	Bivalent/Poised TSS	Fetal Brain Female	brain
33	chr2:172378600-172380600	Active TSS	Fetal Kidney	kidney
34	chr2:172378600-172380600	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
35	chr2:172378600-172380600	Active TSS	Fetal Lung	lung
36	chr2:172378600-172380600	Active TSS	Lung	lung
37	chr2:172378600-172380600	Active TSS	Rectal Smooth Muscle	rectum
38	chr2:172378600-172380600	Active TSS	Stomach Smooth Muscle	stomach
39	chr2:172378600-172380800	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr2:172378600-172380800	Active TSS	Colon Smooth Muscle	Colon
41	chr2:172378600-172380800	Flanking Active TSS	Placenta	Placenta
42	chr2:172378600-172380800	Active TSS	NHDF-Ad	bronchial
43	chr2:172378600-172381000	Active TSS	Aorta	Aorta
44	chr2:172378600-172381000	Flanking Active TSS	Liver	Liver
45	chr2:172378600-172381200	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr2:172378800-172379800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:172378800-172379800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:172378800-172379800	Active TSS	Primary hematopoietic stem cells	blood
49	chr2:172378800-172380000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:172378800-172380200	Active TSS	H1 Cell Line	embryonic stem cell

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