Variant report

Variant	rs9390148
Chromosome Location	chr6:144284502-144284503
allele	A/G
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	USF2	chr6:144284354-144284659	H1-hESC	embryonic stem cell:	n/a	n/a
2	SIN3A	chr6:144284060-144284837	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr6:144284360-144284626	H1-hESC	embryonic stem cell:	n/a	n/a
4	USF1	chr6:144284292-144284675	H1-hESC	embryonic stem cell:	n/a	n/a
5	MXI1	chr6:144284110-144284659	H1-hESC	embryonic stem cell:	n/a	n/a
6	USF1	chr6:144284267-144284666	H1-hESC	embryonic stem cell:	n/a	n/a
7	JUND	chr6:144283773-144284551	H1-hESC	embryonic stem cell:	n/a	chr6:144283885-144283899 chr6:144284214-144284223

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:144280416..144282803-chr6:144283309..144285959,2	MCF-7	breast:

Variant related genes	Relation type
PLAGL1	TF binding region
ENSG00000118495	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11155338	0.95[YRI][hapmap]
rs2092894	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2224152	0.92[CEU][hapmap];0.81[CHB][hapmap];0.94[EUR][1000 genomes]
rs2268448	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9321953	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9321956	0.93[EUR][1000 genomes]
rs9373409	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9376803	0.95[YRI][hapmap]
rs9386053	0.92[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9390147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9390150	0.92[CEU][hapmap];0.95[YRI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9399468	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9403540	1.00[CEU][hapmap];0.88[CHD][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs9403542	0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3408554	chr6:144106707-144369589	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3522138	chr6:144174685-144367463	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv3522139	chr6:144174685-144367463	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv830830	chr6:144177942-144380870	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9390148	PLAGL1	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144258400-144288000	Weak transcription	Primary T cells from cord blood	blood
2	chr6:144261600-144285800	Weak transcription	Small Intestine	intestine
3	chr6:144261600-144287000	Weak transcription	GM12878-XiMat	blood
4	chr6:144269200-144290200	Weak transcription	Fetal Thymus	thymus
5	chr6:144269400-144287400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:144269400-144289600	Weak transcription	Pancreas	Pancrea
7	chr6:144269600-144284800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr6:144269600-144294000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:144269800-144285200	Weak transcription	Spleen	Spleen
10	chr6:144269800-144286000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr6:144269800-144286400	Weak transcription	Right Ventricle	heart
12	chr6:144269800-144286600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:144269800-144289800	Weak transcription	Ovary	ovary
14	chr6:144269800-144296000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:144269800-144304400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:144270400-144284600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:144270400-144284600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr6:144271400-144296800	Weak transcription	Primary B cells from cord blood	blood
19	chr6:144274400-144289800	Weak transcription	Esophagus	oesophagus
20	chr6:144275000-144293000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:144276600-144287000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr6:144277200-144291200	Genic enhancers	Fetal Muscle Leg	muscle
23	chr6:144277600-144287000	Weak transcription	HMEC	breast
24	chr6:144278800-144286600	Weak transcription	NHDF-Ad	bronchial
25	chr6:144280200-144290400	Weak transcription	Fetal Heart	heart
26	chr6:144280400-144287200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
27	chr6:144280400-144287400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
28	chr6:144280400-144288200	Weak transcription	Gastric	stomach
29	chr6:144280400-144291400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr6:144280600-144286000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:144280600-144287800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
32	chr6:144280800-144287800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
33	chr6:144281200-144285200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:144281200-144285400	Enhancers	Fetal Lung	lung
35	chr6:144281200-144286800	Enhancers	Adipose Nuclei	Adipose
36	chr6:144281400-144286000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr6:144281800-144285000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:144281800-144285200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:144281800-144285200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr6:144281800-144286200	Weak transcription	Osteobl	bone
41	chr6:144281800-144294800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr6:144282000-144286000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr6:144282400-144284800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
44	chr6:144282400-144284800	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr6:144282600-144284800	Enhancers	Fetal Brain Male	brain
46	chr6:144282800-144284600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:144283000-144284800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:144283200-144284800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:144283200-144287800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr6:144283400-144284600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell

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