Variant report

Variant	rs7965743
Chromosome Location	chr12:42736822-42736823
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:42730865..42733403-chr12:42735896..42737550,2	MCF-7	breast:
2	chr12:42718314..42720744-chr12:42735500..42738358,4	K562	blood:
3	chr12:42736097..42738418-chr12:42740659..42742927,2	K562	blood:
4	chr12:42717851..42720439-chr12:42735401..42737000,2	K562	blood:

Variant related genes	Relation type
ENSG00000134283	Chromatin interaction
ENSG00000252917	Chromatin interaction
ENSG00000139168	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1051453	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10880283	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880294	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11181398	0.80[EUR][1000 genomes]
rs11181399	0.80[EUR][1000 genomes]
rs11181422	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11181454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11181463	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11181465	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11181466	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11181467	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11181483	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11181499	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11181501	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11181502	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11181507	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12228205	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12308219	0.80[EUR][1000 genomes]
rs12366848	0.83[EUR][1000 genomes]
rs12371762	0.83[EUR][1000 genomes]
rs12423048	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12815283	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12820154	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1551210	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1669886	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1669892	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1669893	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1669904	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1669907	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1669910	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1669936	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17551006	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1796380	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1796381	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1796382	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1796384	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1796386	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1796388	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1796394	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1839935	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2178753	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406674	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2406875	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2600908	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2708058	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708059	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3747558	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3747560	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3810793	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4359266	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4768399	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768402	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768411	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4768413	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55702525	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56051354	0.84[ASN][1000 genomes]
rs56290913	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61926593	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6582395	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6582398	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7133836	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71453350	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7296357	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305397	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7959338	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7969910	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7970003	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048971	chr12:42651976-42801204	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7965743	PPHLN1	Cis_1M	lymphoblastoid	RTeQTL
rs7965743	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42720800-42844400	Weak transcription	Small Intestine	intestine
2	chr12:42721000-42758000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:42721600-42739200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:42721600-42743000	Weak transcription	Esophagus	oesophagus
5	chr12:42721600-42747600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:42721600-42748600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr12:42721600-42750000	Weak transcription	Aorta	Aorta
8	chr12:42721600-42750600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:42721600-42751800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:42721600-42769000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:42721600-42778600	Weak transcription	Spleen	Spleen
12	chr12:42721600-42800800	Weak transcription	Psoas Muscle	Psoas
13	chr12:42721600-42803600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:42721800-42740200	Weak transcription	HSMMtube	muscle
15	chr12:42721800-42745400	Weak transcription	Fetal Brain Male	brain
16	chr12:42721800-42750200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:42721800-42756200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:42721800-42769600	Weak transcription	Brain Substantia Nigra	brain
19	chr12:42721800-42769800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:42721800-42797000	Weak transcription	NHLF	lung
21	chr12:42721800-42803600	Weak transcription	Gastric	stomach
22	chr12:42722000-42737600	Weak transcription	NHDF-Ad	bronchial
23	chr12:42722000-42769600	Weak transcription	Brain Anterior Caudate	brain
24	chr12:42722000-42769600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:42722000-42772600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr12:42722000-42793200	Weak transcription	Fetal Kidney	kidney
27	chr12:42722200-42749800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:42722200-42750200	Weak transcription	Colon Smooth Muscle	Colon
29	chr12:42722200-42752800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:42722200-42769200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr12:42722400-42744600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:42724400-42742200	Weak transcription	Brain Angular Gyrus	brain
33	chr12:42724400-42755400	Weak transcription	Pancreas	Pancrea
34	chr12:42726000-42740200	Weak transcription	Fetal Heart	heart
35	chr12:42726200-42749400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:42729000-42742200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr12:42729600-42738200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:42729600-42738200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:42730400-42750000	Weak transcription	Ovary	ovary
40	chr12:42730600-42737600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr12:42730600-42749800	Weak transcription	Left Ventricle	heart
42	chr12:42730600-42750000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr12:42730800-42737600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:42730800-42737600	Weak transcription	A549	lung
45	chr12:42730800-42742400	Weak transcription	HepG2	liver
46	chr12:42730800-42746800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr12:42730800-42747400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr12:42730800-42748800	Weak transcription	Adipose Nuclei	Adipose
49	chr12:42730800-42769600	Weak transcription	NH-A	brain
50	chr12:42731000-42739000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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