Variant report

Variant	rs10167669
Chromosome Location	chr2:55397523-55397524
allele	C/T
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:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55275252..55277731-chr2:55397374..55401620,4	MCF-7	breast:
2	chr2:55396152..55398981-chr2:55400829..55403298,2	MCF-7	breast:
3	chr2:55396231..55398049-chr2:55458251..55460461,2	K562	blood:
4	chr2:55273899..55278013-chr2:55394987..55400290,7	K562	blood:
5	chr2:55251918..55254652-chr2:55395890..55398049,2	K562	blood:
6	chr2:55269967..55271669-chr2:55397322..55399843,2	K562	blood:
7	chr2:55396357..55398246-chr2:55402197..55406122,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2orf63-1	chr2:55397326-55397546	XLOC_002098

No data

Variant related genes	Relation type
ENSG00000143947	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11692206	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12997656	0.83[ASN][1000 genomes]
rs13021163	0.83[ASN][1000 genomes]
rs4672025	0.81[ASN][1000 genomes]
rs71414550	0.83[ASN][1000 genomes]
rs7580936	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[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	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10167669	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs10167669	CLHC1	cis	Artery Tibial	GTEx
rs10167669	CLHC1	cis	Adipose Subcutaneous	GTEx
rs10167669	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55386800-55416600	Weak transcription	Esophagus	oesophagus
2	chr2:55392800-55400400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:55393000-55404000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:55393000-55422000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:55394000-55419000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:55395200-55400200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:55395400-55398400	Enhancers	Brain Hippocampus Middle	brain
8	chr2:55395400-55400200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:55395600-55399400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:55395600-55399400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:55395600-55400200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:55395600-55400600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:55395600-55400600	Weak transcription	Brain Germinal Matrix	brain
14	chr2:55395600-55412400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:55395600-55422800	Weak transcription	Ovary	ovary
16	chr2:55395600-55427000	Weak transcription	Left Ventricle	heart
17	chr2:55395800-55398600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr2:55395800-55400000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:55395800-55400200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:55395800-55400200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:55395800-55400200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:55395800-55400600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:55395800-55400600	Weak transcription	Fetal Kidney	kidney
24	chr2:55395800-55402400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:55395800-55403000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:55395800-55403000	Weak transcription	Fetal Brain Male	brain
27	chr2:55395800-55418200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr2:55395800-55418400	Weak transcription	Fetal Intestine Large	intestine
29	chr2:55395800-55427000	Weak transcription	Aorta	Aorta
30	chr2:55396000-55400600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:55396200-55400200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:55396200-55402600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr2:55396200-55407400	Weak transcription	HepG2	liver
34	chr2:55396400-55398000	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr2:55396400-55400800	Weak transcription	Fetal Lung	lung
36	chr2:55396400-55402600	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:55397000-55402400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:55397000-55402400	Weak transcription	Brain Angular Gyrus	brain
39	chr2:55397000-55402400	Weak transcription	NHDF-Ad	bronchial
40	chr2:55397000-55410000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:55397200-55397600	Enhancers	Stomach Mucosa	stomach
42	chr2:55397200-55402600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:55397200-55402600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr2:55397200-55450000	Weak transcription	NH-A	brain
45	chr2:55397400-55399200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:55397400-55402600	Weak transcription	NHLF	lung
47	chr2:55397400-55402600	Weak transcription	Osteobl	bone
48	chr2:55397400-55402800	Weak transcription	Brain Anterior Caudate	brain
49	chr2:55397400-55402800	Weak transcription	Brain Substantia Nigra	brain
50	chr2:55397400-55403000	Weak transcription	HSMM	muscle

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