Variant report

Variant	rs13374442
Chromosome Location	chr1:212307858-212307859
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10863941	0.81[ASN][1000 genomes]
rs11579154	0.86[GIH][hapmap]
rs11809969	0.84[ASN][1000 genomes]
rs12043586	0.82[ASN][1000 genomes]
rs2884459	0.81[ASN][1000 genomes]
rs4245745	0.81[ASN][1000 genomes]
rs4951571	0.81[ASN][1000 genomes]
rs4951572	0.82[ASN][1000 genomes]
rs6699232	0.83[ASN][1000 genomes]
rs9651112	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs982091	0.93[CEU][hapmap];0.87[EUR][1000 genomes]

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	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13374442	CD55	cis	cerebellum	SCAN
rs13374442	LPGAT1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212274400-212308200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:212281200-212308400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:212285600-212311200	Weak transcription	Hela-S3	cervix
4	chr1:212287400-212320600	Weak transcription	A549	lung
5	chr1:212292600-212314600	Weak transcription	Thymus	Thymus
6	chr1:212293200-212313200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:212298600-212312200	Weak transcription	Gastric	stomach
8	chr1:212298800-212308200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:212299000-212308000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:212299000-212313000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:212299200-212314200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:212299800-212308600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr1:212300000-212308400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:212300000-212320800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:212300800-212314800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:212301000-212308000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:212301000-212321000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:212304000-212316400	Weak transcription	Fetal Stomach	stomach
19	chr1:212305800-212308400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:212305800-212309000	Weak transcription	HepG2	liver
21	chr1:212307200-212308400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:212307200-212313000	Weak transcription	Dnd41	blood
23	chr1:212307800-212308000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:212307800-212308800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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