Variant report

Variant	rs3828668
Chromosome Location	chr5:126365228-126365229
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:126364877..126368459-chr5:126407436..126411131,4	MCF-7	breast:
2	chr5:126113643..126115692-chr5:126362942..126365785,2	K562	blood:
3	chr5:126181847..126184918-chr5:126362668..126365476,3	K562	blood:
4	chr5:126213898..126216228-chr5:126364824..126367570,2	K562	blood:
5	chr5:126364290..126367111-chr5:126408529..126412360,4	MCF-7	breast:
6	chr5:126364050..126367985-chr5:126407589..126410597,4	K562	blood:
7	chr5:126362711..126365443-chr5:126540946..126543546,2	MCF-7	breast:
8	chr5:126112502..126115238-chr5:126364683..126367658,2	MCF-7	breast:
9	chr5:126112473..126115233-chr5:126364397..126368675,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000173926	Chromatin interaction
ENSG00000113368	Chromatin interaction
ENSG00000164241	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13163601	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2240800	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34150806	0.86[AFR][1000 genomes]
rs9637916	0.93[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024265	chr5:126213004-126691163	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv869897	chr5:126224358-126445210	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3828668	C5orf63	cis	Nerve Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126362800-126367200	Active TSS	Right Ventricle	heart
2	chr5:126363000-126367200	Active TSS	HSMM	muscle
3	chr5:126364200-126365400	Flanking Active TSS	HUVEC	blood vessel
4	chr5:126364200-126366000	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr5:126364200-126366000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:126364200-126366800	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr5:126364400-126365400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:126364400-126365400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
9	chr5:126364400-126365400	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr5:126364400-126365400	Flanking Active TSS	Osteobl	bone
11	chr5:126364400-126365600	Flanking Active TSS	Primary B cells from peripheral blood	blood
12	chr5:126364400-126365600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr5:126364400-126365600	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr5:126364400-126365600	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr5:126364400-126365600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
16	chr5:126364400-126365600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr5:126364400-126365600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
18	chr5:126364400-126365800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr5:126364400-126366000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:126364400-126366000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr5:126364400-126366000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:126364400-126366800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:126364400-126366800	Active TSS	Brain Hippocampus Middle	brain
24	chr5:126364400-126366800	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr5:126364400-126367000	Active TSS	Left Ventricle	heart
26	chr5:126364400-126367000	Active TSS	Lung	lung
27	chr5:126364400-126367000	Active TSS	K562	blood
28	chr5:126364400-126367200	Active TSS	Brain Anterior Caudate	brain
29	chr5:126364400-126367200	Active TSS	Right Atrium	heart
30	chr5:126364400-126367200	Bivalent/Poised TSS	Thymus	Thymus
31	chr5:126364600-126365400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
32	chr5:126364600-126365400	Flanking Active TSS	Fetal Heart	heart
33	chr5:126364600-126365400	Bivalent/Poised TSS	Fetal Kidney	kidney
34	chr5:126364600-126365400	Enhancers	Stomach Mucosa	stomach
35	chr5:126364600-126365400	Enhancers	Spleen	Spleen
36	chr5:126364600-126365600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
37	chr5:126364600-126365600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:126364600-126365800	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr5:126364600-126366600	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr5:126364600-126366800	Bivalent/Poised TSS	Fetal Stomach	stomach
41	chr5:126364600-126367000	Active TSS	Brain Cingulate Gyrus	brain
42	chr5:126364600-126367200	Active TSS	Brain Angular Gyrus	brain
43	chr5:126364800-126365400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
44	chr5:126364800-126365400	Active TSS	Fetal Brain Female	brain
45	chr5:126364800-126365400	Flanking Active TSS	NH-A	brain
46	chr5:126364800-126365600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr5:126364800-126365600	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
48	chr5:126364800-126367000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:126364800-126367000	Active TSS	Ovary	ovary
50	chr5:126364800-126367200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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