Variant report

Variant	rs4667682
Chromosome Location	chr2:172127920-172127921
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172126634..172129658-chr2:172132451..172134211,3	MCF-7	breast:
2	chr2:172124703..172126558-chr2:172126623..172128823,2	MCF-7	breast:
3	chr2:172123232..172126602-chr2:172127090..172129825,3	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs17218110	0.94[AMR][1000 genomes]
rs17283817	0.81[AMR][1000 genomes]
rs1861769	0.96[AMR][1000 genomes]
rs1861770	0.93[AMR][1000 genomes]
rs62169054	0.92[AMR][1000 genomes]
rs6433287	0.89[ASN][1000 genomes]
rs6747959	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72625231	0.94[AMR][1000 genomes]
rs72625232	0.87[ASN][1000 genomes]
rs9653290	0.92[AMR][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	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Hippocampal atrophy	22745009	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4667682	SP3	cis	cerebellum	SCAN
rs4667682	XIRP2	cis	cerebellum	SCAN
rs4667682	HAT1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172119000-172128200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr2:172125400-172128600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:172126800-172128600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:172126800-172128800	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr2:172127000-172128000	Enhancers	NHEK	skin
6	chr2:172127000-172129000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr2:172127400-172129800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:172127600-172128000	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr2:172127600-172128800	Enhancers	Fetal Brain Male	brain
10	chr2:172127600-172129000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:172127600-172129000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr2:172127600-172129000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:172127600-172129200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr2:172127600-172130000	Enhancers	HMEC	breast
15	chr2:172127600-172130400	Enhancers	Colon Smooth Muscle	Colon
16	chr2:172127800-172128200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:172127800-172128800	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr2:172127800-172129000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:172127800-172129000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:172127800-172129000	Enhancers	NHDF-Ad	bronchial
21	chr2:172127800-172129200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:172127800-172129200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr2:172127800-172129200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:172127800-172129200	Flanking Active TSS	A549	lung
25	chr2:172127800-172129800	Enhancers	Hela-S3	cervix
26	chr2:172127800-172134000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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