Variant report

Variant	rs12126717
Chromosome Location	chr1:165512059-165512060
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr1:165511461-165512220	HepG2	liver:	n/a	chr1:165511663-165511674 chr1:165512053-165512067 chr1:165511658-165511674 chr1:165512050-165512066 chr1:165511663-165511674 chr1:165512054-165512065 chr1:165512089-165512105 chr1:165512090-165512104 chr1:165511658-165511673 chr1:165511661-165511675 chr1:165511662-165511673
2	FOXA1	chr1:165511913-165512183	T-47D	breast:	n/a	chr1:165512098-165512110 chr1:165512036-165512051
3	MAFF	chr1:165511447-165512192	K562	blood:	n/a	chr1:165512090-165512104 chr1:165511657-165511675
4	MAFK	chr1:165512054-165512240	H1-hESC	embryonic stem cell:	n/a	chr1:165512054-165512065 chr1:165512089-165512105 chr1:165512090-165512104
5	MAFK	chr1:165511475-165512219	IMR90	lung:	n/a	chr1:165511663-165511674 chr1:165512053-165512067 chr1:165511658-165511674 chr1:165512050-165512066 chr1:165511663-165511674 chr1:165512054-165512065 chr1:165512089-165512105 chr1:165512090-165512104 chr1:165511658-165511673 chr1:165511661-165511675 chr1:165511662-165511673
6	MAFK	chr1:165511995-165512141	Hela-S3	cervix:	n/a	chr1:165512053-165512067 chr1:165512050-165512066 chr1:165512054-165512065 chr1:165512089-165512105 chr1:165512090-165512104
7	MAFK	chr1:165511485-165512205	K562	blood:	n/a	chr1:165511663-165511674 chr1:165512053-165512067 chr1:165511658-165511674 chr1:165512050-165512066 chr1:165511663-165511674 chr1:165512054-165512065 chr1:165512089-165512105 chr1:165512090-165512104 chr1:165511658-165511673 chr1:165511661-165511675 chr1:165511662-165511673
8	ESR1	chr1:165511882-165512131	T-47D	breast:	n/a	n/a
9	BACH1	chr1:165512041-165512142	H1-hESC	embryonic stem cell:	n/a	n/a
10	FOXA1	chr1:165511915-165512177	T-47D	breast:	n/a	chr1:165512098-165512110 chr1:165512036-165512051
11	MAFF	chr1:165511441-165512246	HepG2	liver:	n/a	chr1:165512090-165512104 chr1:165511657-165511675
12	MAFK	chr1:165511474-165512268	HepG2	liver:	n/a	chr1:165511663-165511674 chr1:165512053-165512067 chr1:165511658-165511674 chr1:165512050-165512066 chr1:165511663-165511674 chr1:165512054-165512065 chr1:165512089-165512105 chr1:165512090-165512104 chr1:165511658-165511673 chr1:165511661-165511675 chr1:165511662-165511673

Variant related genes	Relation type
ENSG00000237463	TF binding region
LRRC52	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1011469	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1025159	0.91[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap]
rs1157861	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12117066	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12137629	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12143824	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12143868	0.80[ASN][1000 genomes]
rs1326374	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409413	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1425753	0.91[ASN][1000 genomes]
rs16846547	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16846623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846756	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16847073	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16847083	0.91[ASN][1000 genomes]
rs16847085	0.91[ASN][1000 genomes]
rs16847110	0.91[ASN][1000 genomes]
rs16847331	0.92[CHB][hapmap]
rs16847570	0.84[CHB][hapmap]
rs1913836	0.92[CHB][hapmap]
rs2152818	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2252342	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2478262	0.81[ASN][1000 genomes]
rs2553637	0.81[ASN][1000 genomes]
rs285421	0.91[ASN][1000 genomes]
rs285422	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs285435	0.97[ASN][1000 genomes]
rs285438	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs285462	0.83[ASN][1000 genomes]
rs285467	0.83[ASN][1000 genomes]
rs285468	0.83[ASN][1000 genomes]
rs285473	0.81[ASN][1000 genomes]
rs285474	0.81[ASN][1000 genomes]
rs285478	0.81[ASN][1000 genomes]
rs285479	0.81[ASN][1000 genomes]
rs34201742	0.88[ASN][1000 genomes]
rs401457	0.83[ASN][1000 genomes]
rs41267552	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41267554	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4147146	0.91[CHB][hapmap]
rs55890197	0.85[ASN][1000 genomes]
rs55957417	0.90[ASN][1000 genomes]
rs56201005	0.90[ASN][1000 genomes]
rs56277222	0.91[ASN][1000 genomes]
rs57799548	0.88[ASN][1000 genomes]
rs58058936	0.90[ASN][1000 genomes]
rs6662135	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6669449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696050	0.90[ASN][1000 genomes]
rs722260	0.90[ASN][1000 genomes]
rs72693816	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72693826	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74120755	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7521982	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7533908	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7535829	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7535979	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7539622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554080	0.84[CHB][hapmap]
rs927844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12126717	LRRC52	cis	Stomach	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165505600-165513000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:165507600-165512800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:165510200-165513000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:165510400-165512400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:165510400-165512800	Weak transcription	Adipose Nuclei	Adipose
6	chr1:165510400-165512800	Weak transcription	Placenta	Placenta
7	chr1:165510400-165512800	Weak transcription	Right Atrium	heart
8	chr1:165510400-165512800	Weak transcription	Right Ventricle	heart
9	chr1:165510400-165513000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:165510600-165512800	Weak transcription	Left Ventricle	heart
11	chr1:165510600-165512800	Weak transcription	Psoas Muscle	Psoas
12	chr1:165510600-165513000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:165511000-165512800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:165511200-165512800	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr1:165511400-165512200	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr1:165511400-165512800	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:165511400-165513800	Enhancers	Fetal Lung	lung
18	chr1:165511400-165514200	Enhancers	Fetal Heart	heart
19	chr1:165511800-165512800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:165511800-165512800	Weak transcription	Fetal Kidney	kidney
21	chr1:165511800-165512800	Weak transcription	Gastric	stomach
22	chr1:165511800-165513000	Enhancers	Fetal Stomach	stomach
23	chr1:165512000-165512200	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr1:165512000-165512400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:165512000-165512400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr1:165512000-165512800	Weak transcription	Stomach Mucosa	stomach

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