Variant report

Variant	rs4951572
Chromosome Location	chr1:212302904-212302905
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10863941	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10863942	0.96[ASN][1000 genomes]
rs11809969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12042024	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12043586	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13374442	0.82[ASN][1000 genomes]
rs1826156	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2884459	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4245745	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4951568	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4951571	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6540721	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6699232	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7523723	0.80[AMR][1000 genomes];0.94[ASN][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
rs4951572	LPGAT1	cis	cerebellum	SCAN
rs4951572	RTN3	trans	parietal	SCAN

Chromatin state (count:32 , 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	chr1:212285000-212303200	Weak transcription	Fetal Stomach	stomach
4	chr1:212285600-212311200	Weak transcription	Hela-S3	cervix
5	chr1:212287400-212320600	Weak transcription	A549	lung
6	chr1:212292600-212314600	Weak transcription	Thymus	Thymus
7	chr1:212293200-212313200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:212295400-212303800	Weak transcription	K562	blood
9	chr1:212298200-212307200	Strong transcription	Dnd41	blood
10	chr1:212298600-212303400	Weak transcription	Fetal Intestine Small	intestine
11	chr1:212298600-212305600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:212298600-212306200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:212298600-212312200	Weak transcription	Gastric	stomach
14	chr1:212298800-212308200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:212299000-212305200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:212299000-212308000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:212299000-212313000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:212299200-212305000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:212299200-212305000	Weak transcription	Fetal Thymus	thymus
20	chr1:212299200-212307800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:212299200-212314200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:212299800-212308600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr1:212300000-212308400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:212300000-212320800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:212300800-212304000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:212300800-212306200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:212300800-212314800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:212301000-212303000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:212301000-212305600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:212301000-212308000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:212301000-212321000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:212302800-212307400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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