Variant report

Variant	rs9373409
Chromosome Location	chr6:144287218-144287219
allele	C/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	TCF12	chr6:144287126-144287388	H1-hESC	embryonic stem cell:	n/a	n/a
2	TEAD4	chr6:144287107-144287411	H1-hESC	embryonic stem cell:	n/a	n/a
3	JUND	chr6:144287067-144287257	K562	blood:	n/a	chr6:144287136-144287146 chr6:144287137-144287145 chr6:144287136-144287146
4	ATF1	chr6:144286990-144287278	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:144286319..144288248-chr6:144317369..144319699,2	K562	blood:
2	chr6:144286646..144289265-chr6:144304089..144305699,2	K562	blood:
3	chr6:143832151..143834228-chr6:144285681..144288374,2	MCF-7	breast:
4	chr6:144286109..144288326-chr6:144291907..144294386,3	K562	blood:

Variant related genes	Relation type
PLAGL1	TF binding region
ENSG00000001036	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	0.83[YRI][hapmap]
rs2092894	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2224152	0.85[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs2268448	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9321953	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9321956	0.87[EUR][1000 genomes]
rs9376803	0.83[YRI][hapmap]
rs9386053	0.86[ASW][hapmap];0.93[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9390147	0.93[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9390148	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]
rs9390150	0.85[CEU][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes]
rs9399468	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs9403540	0.93[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs9403542	0.83[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
rs9373409	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	chr6:144269200-144290200	Weak transcription	Fetal Thymus	thymus
3	chr6:144269400-144287400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:144269400-144289600	Weak transcription	Pancreas	Pancrea
5	chr6:144269600-144294000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr6:144269800-144289800	Weak transcription	Ovary	ovary
7	chr6:144269800-144296000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:144269800-144304400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:144271400-144296800	Weak transcription	Primary B cells from cord blood	blood
10	chr6:144274400-144289800	Weak transcription	Esophagus	oesophagus
11	chr6:144275000-144293000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:144277200-144291200	Genic enhancers	Fetal Muscle Leg	muscle
13	chr6:144280200-144290400	Weak transcription	Fetal Heart	heart
14	chr6:144280400-144287400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
15	chr6:144280400-144288200	Weak transcription	Gastric	stomach
16	chr6:144280400-144291400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr6:144280600-144287800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
18	chr6:144280800-144287800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
19	chr6:144281800-144294800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr6:144283200-144287800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:144283800-144287400	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:144284200-144287400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:144284200-144287800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
24	chr6:144284200-144289000	Weak transcription	NHLF	lung
25	chr6:144284600-144288200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
26	chr6:144284600-144288400	Strong transcription	Stomach Smooth Muscle	stomach
27	chr6:144284600-144290600	Weak transcription	Primary B cells from peripheral blood	blood
28	chr6:144284800-144287800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
29	chr6:144284800-144294400	Weak transcription	Fetal Brain Male	brain
30	chr6:144284800-144318400	Weak transcription	Aorta	Aorta
31	chr6:144285000-144287400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
32	chr6:144285000-144287800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:144285000-144292400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:144285200-144287400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:144285200-144288400	Strong transcription	Primary hematopoietic stem cells	blood
36	chr6:144285200-144289000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:144285400-144291400	Weak transcription	Colonic Mucosa	Colon
38	chr6:144285400-144294200	Weak transcription	Left Ventricle	heart
39	chr6:144285800-144293400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:144286000-144287600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr6:144286000-144288400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:144286000-144290400	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr6:144286200-144287800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:144286200-144289800	Weak transcription	Right Atrium	heart
45	chr6:144286400-144287600	Genic enhancers	Fetal Lung	lung
46	chr6:144286400-144288200	Weak transcription	Fetal Kidney	kidney
47	chr6:144286400-144288400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:144286400-144288600	Genic enhancers	Placenta	Placenta
49	chr6:144286600-144287600	Genic enhancers	Osteobl	bone
50	chr6:144286600-144288200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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