Variant report

Variant	rs1924379
Chromosome Location	chr13:38443712-38443713
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1337601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415601	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1538145	0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs1538146	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1538148	0.86[CHD][hapmap]
rs1819607	0.88[CEU][hapmap]
rs2323637	0.84[ASN][1000 genomes]
rs2323638	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3812837	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3812840	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4144140	0.86[CHD][hapmap];0.84[ASN][1000 genomes]
rs942345	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9532131	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9548087	0.83[ASN][1000 genomes]
rs9566272	0.84[ASN][1000 genomes]
rs9576388	0.91[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[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	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1924379	SMAD9	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38440000-38444600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr13:38440400-38445000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr13:38440600-38445200	Active TSS	Fetal Brain Female	brain
4	chr13:38441000-38444600	Active TSS	H1 Cell Line	embryonic stem cell
5	chr13:38441000-38444600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr13:38441400-38444600	Active TSS	NHDF-Ad	bronchial
7	chr13:38441600-38444600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr13:38441600-38444600	Active TSS	Osteobl	bone
9	chr13:38442000-38444600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr13:38442000-38444800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr13:38442200-38444200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:38442200-38444600	Active TSS	NH-A	brain
13	chr13:38442200-38445200	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr13:38442400-38444200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr13:38442400-38444400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr13:38442400-38445200	Active TSS	Ovary	ovary
17	chr13:38442800-38444000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr13:38442800-38444000	Bivalent/Poised TSS	NHLF	lung
19	chr13:38442800-38444200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr13:38442800-38444200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr13:38442800-38444400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr13:38442800-38444400	Active TSS	Brain Anterior Caudate	brain
23	chr13:38442800-38444400	Active TSS	Fetal Kidney	kidney
24	chr13:38442800-38444400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
25	chr13:38442800-38444600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr13:38442800-38444600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr13:38442800-38444600	Active TSS	H9 Cell Line	embryonic stem cell
28	chr13:38442800-38444600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr13:38442800-38444800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr13:38442800-38444800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
31	chr13:38442800-38444800	Active TSS	Brain Substantia Nigra	brain
32	chr13:38442800-38444800	Active TSS	Colon Smooth Muscle	Colon
33	chr13:38442800-38444800	Active TSS	Right Ventricle	heart
34	chr13:38442800-38445000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
35	chr13:38442800-38445200	Active TSS	Right Atrium	heart
36	chr13:38442800-38445400	Active TSS	Brain Angular Gyrus	brain
37	chr13:38443000-38443800	Bivalent/Poised TSS	HSMM	muscle
38	chr13:38443000-38444000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr13:38443000-38444200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr13:38443000-38444200	Bivalent/Poised TSS	Fetal Stomach	stomach
41	chr13:38443000-38444400	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
42	chr13:38443000-38444600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr13:38443000-38444600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr13:38443000-38444600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
45	chr13:38443000-38444600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
46	chr13:38443000-38444600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
47	chr13:38443000-38444600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
48	chr13:38443000-38444600	Bivalent/Poised TSS	HSMMtube	muscle
49	chr13:38443000-38444800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
50	chr13:38443000-38444800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain

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