Variant report

Variant	rs3829790
Chromosome Location	chr1:160920809-160920810
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10908815	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11265510	0.80[MEX][hapmap]
rs11265522	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11265526	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11265533	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11265534	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11265535	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11587040	0.81[MEX][hapmap]
rs11805631	0.87[AMR][1000 genomes]
rs12126310	0.85[CHB][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1855186	0.85[MEX][hapmap]
rs1981048	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2039415	0.81[MEX][hapmap]
rs2184066	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28368883	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34655593	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3928803	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3928804	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4656958	0.81[MEX][hapmap]
rs4656968	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4656971	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4656972	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61802165	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6656769	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6680969	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6691389	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7411035	0.85[MEX][hapmap]
rs7516660	0.81[MEX][hapmap]
rs7526396	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs955615	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3829790	SPTA1	cis	parietal	SCAN
rs3829790	F11R	cis	parietal	SCAN
rs3829790	APCS	cis	cerebellum	SCAN
rs3829790	SLAMF9	cis	parietal	SCAN
rs3829790	C1orf110	cis	cerebellum	SCAN
rs3829790	LMNA	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160916600-160921800	Enhancers	Fetal Intestine Large	intestine
2	chr1:160916800-160923800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:160917600-160921800	Enhancers	A549	lung
4	chr1:160918000-160921400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:160918000-160923800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:160918200-160921000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:160918200-160921200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:160918200-160923800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:160918400-160921600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr1:160918600-160921000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:160918800-160921000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:160919000-160924000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:160919000-160924400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:160919400-160921800	Enhancers	Fetal Intestine Small	intestine
15	chr1:160919400-160923000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:160919600-160921600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:160919600-160921600	Enhancers	NHEK	skin
18	chr1:160919600-160924200	Enhancers	HMEC	breast
19	chr1:160919800-160921800	Enhancers	Ovary	ovary
20	chr1:160919800-160921800	Enhancers	Right Atrium	heart
21	chr1:160919800-160923200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr1:160919800-160924000	Weak transcription	Fetal Heart	heart
23	chr1:160920000-160921000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:160920000-160921400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:160920000-160923600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:160920200-160924200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:160920400-160921200	Enhancers	Left Ventricle	heart
28	chr1:160920400-160921400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:160920400-160921400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:160920600-160921000	Weak transcription	HepG2	liver
31	chr1:160920600-160921400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:160920600-160922800	Weak transcription	Right Ventricle	heart
33	chr1:160920800-160921200	Enhancers	Fetal Muscle Leg	muscle
34	chr1:160920800-160921400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:160920800-160921800	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr1:160920800-160921800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:160920800-160921800	Enhancers	Esophagus	oesophagus
38	chr1:160920800-160921800	Enhancers	Fetal Muscle Trunk	muscle

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