Variant report

Variant	rs7965392
Chromosome Location	chr12:42540280-42540281
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:42539891..42542441-chr12:42748681..42750572,2	MCF-7	breast:
2	chr12:42536858..42540358-chr12:42630016..42633914,10	MCF-7	breast:
3	chr12:42537125..42540322-chr12:42717377..42722308,7	MCF-7	breast:
4	chr12:42537957..42540928-chr12:42622624..42625244,2	MCF-7	breast:
5	chr12:42535865..42541158-chr12:42630084..42634162,10	K562	blood:
6	chr12:42536195..42540644-chr12:42629191..42634148,6	K562	blood:
7	chr12:42539265..42541316-chr12:42719076..42720974,2	K562	blood:
8	chr12:42537508..42540547-chr12:42555328..42558210,3	MCF-7	breast:
9	chr12:42537037..42538708-chr12:42539498..42541972,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000269367	Chromatin interaction
ENSG00000151233	Chromatin interaction
ENSG00000015153	Chromatin interaction
ENSG00000139168	Chromatin interaction
ENSG00000134283	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10459290	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10492388	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1059360	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10785333	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10785334	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10880256	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10880258	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10880259	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10880260	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10880261	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10880264	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10880268	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10880269	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10880272	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10880273	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11181328	0.87[ASN][1000 genomes]
rs11181364	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11181378	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11181380	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11181398	0.80[EUR][1000 genomes]
rs11181399	0.80[EUR][1000 genomes]
rs12049942	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12308219	0.80[EUR][1000 genomes]
rs12370778	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12371615	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12372623	0.89[ASN][1000 genomes]
rs2406567	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2406568	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6582390	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6582391	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7138877	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7312933	0.86[ASN][1000 genomes]
rs7315968	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7957471	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7974476	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7974654	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7977365	0.87[ASN][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	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7965392	PPHLN1	Cis_1M	lymphoblastoid	RTeQTL
rs7965392	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42539200-42552200	Weak transcription	HSMM	muscle
2	chr12:42539200-42563800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:42539400-42540400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:42539400-42541000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:42539400-42551400	Weak transcription	Primary B cells from cord blood	blood
6	chr12:42539400-42551800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:42539400-42554000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:42539400-42554200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr12:42539400-42556000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr12:42539400-42577000	Weak transcription	Aorta	Aorta
11	chr12:42539400-42583200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:42539600-42540400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr12:42539600-42540600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:42539600-42550200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:42539600-42550800	Weak transcription	Primary T cells from cord blood	blood
16	chr12:42539600-42550800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr12:42539600-42551600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:42539600-42551800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr12:42539600-42552200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:42539600-42552400	Weak transcription	HUVEC	blood vessel
21	chr12:42539600-42553600	Weak transcription	Adipose Nuclei	Adipose
22	chr12:42539600-42553800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:42539600-42553800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:42539600-42555800	Weak transcription	Brain Substantia Nigra	brain
25	chr12:42539600-42556200	Weak transcription	HSMMtube	muscle
26	chr12:42539600-42574000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:42539600-42578400	Weak transcription	Left Ventricle	heart
28	chr12:42539600-42586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:42539800-42540400	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr12:42539800-42540400	Enhancers	K562	blood
31	chr12:42539800-42541000	Enhancers	A549	lung
32	chr12:42539800-42550600	Weak transcription	Fetal Lung	lung
33	chr12:42539800-42550800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:42539800-42551600	Weak transcription	GM12878-XiMat	blood
35	chr12:42539800-42551800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr12:42539800-42551800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr12:42539800-42553000	Weak transcription	Hela-S3	cervix
38	chr12:42539800-42554200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr12:42539800-42568600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr12:42539800-42569000	Weak transcription	Fetal Kidney	kidney
41	chr12:42539800-42582800	Weak transcription	Spleen	Spleen
42	chr12:42539800-42607800	Weak transcription	Pancreas	Pancrea
43	chr12:42540000-42540400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
44	chr12:42540000-42540400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
45	chr12:42540000-42540400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr12:42540000-42550600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:42540000-42552200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:42540000-42552200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:42540000-42553800	Weak transcription	Primary B cells from peripheral blood	blood
50	chr12:42540000-42556000	Weak transcription	Fetal Intestine Small	intestine

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