Variant report

Variant	rs1409413
Chromosome Location	chr1:165530932-165530933
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1011469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1025159	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs1157861	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12117066	0.84[EUR][1000 genomes]
rs12126717	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12137629	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12143824	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12239745	0.81[AFR][1000 genomes]
rs1326374	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1425753	0.83[ASN][1000 genomes]
rs16846547	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16846623	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16846756	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16847073	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847083	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847085	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847110	1.00[ASN][1000 genomes]
rs16847331	0.92[CHB][hapmap]
rs16847570	0.84[CHB][hapmap]
rs1913836	0.92[CHB][hapmap]
rs2152818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252342	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28473212	0.81[AFR][1000 genomes]
rs285421	0.83[ASN][1000 genomes]
rs285422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs285435	0.94[ASN][1000 genomes]
rs285438	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs34201742	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41267552	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41267554	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4147146	0.91[CHB][hapmap];0.80[AMR][1000 genomes]
rs55890197	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55957417	0.98[ASN][1000 genomes]
rs56201005	0.98[ASN][1000 genomes]
rs56277222	1.00[ASN][1000 genomes]
rs57799548	0.97[ASN][1000 genomes]
rs58058936	0.98[ASN][1000 genomes]
rs6657863	0.83[CEU][hapmap]
rs6669449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6696050	0.98[ASN][1000 genomes]
rs722260	0.99[ASN][1000 genomes]
rs72693816	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72693826	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs74120755	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7521982	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7533908	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7535829	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7535979	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7539622	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7554080	0.84[CHB][hapmap]
rs927844	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1409413	LRRC52	cis	Esophagus Muscularis	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165529600-165531200	Enhancers	Fetal Lung	lung
2	chr1:165529600-165531400	Enhancers	Fetal Heart	heart
3	chr1:165529800-165531000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
4	chr1:165529800-165531000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:165529800-165531000	Enhancers	Brain Anterior Caudate	brain
6	chr1:165529800-165531200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:165529800-165531200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
8	chr1:165529800-165531200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:165529800-165531200	Enhancers	Right Ventricle	heart
10	chr1:165530000-165531000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr1:165530000-165531000	Enhancers	Fetal Brain Male	brain
12	chr1:165530000-165531200	Enhancers	Ovary	ovary
13	chr1:165530200-165531000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
14	chr1:165530200-165531000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
15	chr1:165530200-165531400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
16	chr1:165530600-165531000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
17	chr1:165530600-165531000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:165530600-165531000	Flanking Active TSS	Brain Germinal Matrix	brain
19	chr1:165530800-165531000	Enhancers	Brain Substantia Nigra	brain
20	chr1:165530800-165533600	Weak transcription	Left Ventricle	heart
21	chr1:165530800-165533800	Weak transcription	Right Atrium	heart

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