Variant report

Variant	rs10489505
Chromosome Location	chr1:84268144-84268145
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TTLL7-2	chr1:84267199-84268934	ENSG00000233008

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1010436	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10437027	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10489500	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11802417	0.93[ASN][1000 genomes]
rs12728131	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12728368	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12735437	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12736562	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12742875	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12744687	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12744886	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12746729	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12748928	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12754424	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1324487	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1569748	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17520771	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17521573	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17521594	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17521713	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17522440	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17578175	0.93[AMR][1000 genomes]
rs17580638	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17580799	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17581022	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2143756	0.81[AMR][1000 genomes]
rs2143757	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2147391	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34561331	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35260485	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35531285	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35729141	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35906154	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36120300	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3946083	0.81[AMR][1000 genomes]
rs6663404	0.81[AMR][1000 genomes]
rs71652653	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71652654	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10489505	CLCA1	cis	parietal	SCAN
rs10489505	PRKACB	cis	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84262800-84268800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:84264200-84268400	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr1:84265200-84268200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:84265600-84268400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:84265800-84268200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:84265800-84268200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:84265800-84268400	Weak transcription	Right Atrium	heart
8	chr1:84265800-84268600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:84265800-84270400	Weak transcription	Pancreas	Pancrea
10	chr1:84266000-84268200	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:84267200-84268800	Enhancers	Stomach Smooth Muscle	stomach
12	chr1:84267600-84268600	Enhancers	Fetal Brain Female	brain
13	chr1:84267600-84268800	Enhancers	Liver	Liver
14	chr1:84267600-84268800	Enhancers	Colon Smooth Muscle	Colon
15	chr1:84267600-84268800	Enhancers	Fetal Heart	heart
16	chr1:84267600-84269400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:84267800-84268400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr1:84267800-84268800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:84267800-84268800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:84267800-84268800	Enhancers	Adipose Nuclei	Adipose
21	chr1:84267800-84268800	Enhancers	Aorta	Aorta
22	chr1:84267800-84268800	Enhancers	Right Ventricle	heart
23	chr1:84267800-84269200	Enhancers	Fetal Intestine Large	intestine
24	chr1:84267800-84269400	Enhancers	Fetal Intestine Small	intestine
25	chr1:84268000-84268400	Enhancers	Duodenum Mucosa	Duodenum
26	chr1:84268000-84268400	Enhancers	Small Intestine	intestine
27	chr1:84268000-84268800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:84268000-84269400	Enhancers	Pancreatic Islets	Pancreatic Islet

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