Variant report

Variant	rs1540131
Chromosome Location	chr13:39452235-39452236
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:15)

rs_ID	r²[population]
rs11616774	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11618539	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1894105	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1945502	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1945511	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2027770	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2226913	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4146172	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4943613	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945502	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6563646	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563647	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7324518	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9548465	0.83[CEU][hapmap]
rs9548509	0.84[EUR][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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1540131	DCLK1	cis	parietal	SCAN
rs1540131	GPR109B	trans	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39419200-39452600	Weak transcription	Fetal Intestine Large	intestine
2	chr13:39420800-39454600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr13:39424200-39457800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr13:39430600-39458000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr13:39430600-39462400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr13:39432200-39458200	Weak transcription	Gastric	stomach
7	chr13:39432600-39468600	Weak transcription	Psoas Muscle	Psoas
8	chr13:39433800-39456600	Weak transcription	Fetal Stomach	stomach
9	chr13:39436000-39457800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr13:39443600-39452800	Weak transcription	Liver	Liver
11	chr13:39446400-39458000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr13:39447000-39457800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr13:39447000-39458800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr13:39447000-39462400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr13:39447000-39462400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr13:39449200-39453600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr13:39449400-39457000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr13:39449600-39453000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr13:39449800-39454600	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr13:39450000-39453000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr13:39450000-39453400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr13:39450000-39455000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr13:39450000-39456400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr13:39450600-39454600	Weak transcription	Pancreas	Pancrea
25	chr13:39450600-39457800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr13:39451200-39455600	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr13:39451400-39468200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr13:39451600-39452800	Weak transcription	Fetal Kidney	kidney
29	chr13:39452000-39453400	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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