Variant report

Variant	rs9496542
Chromosome Location	chr6:143569589-143569590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:143565573..143568221-chr6:143568963..143571778,2	MCF-7	breast:
2	chr6:143568655..143572983-chr6:143580340..143584023,4	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1559598	1.00[CHB][hapmap]
rs1570350	0.86[ASW][hapmap]
rs1863137	1.00[CHB][hapmap]
rs1885649	1.00[ASW][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs2328474	1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs62429641	1.00[ASN][1000 genomes]
rs6901152	1.00[CHB][hapmap];0.94[MKK][hapmap]
rs6907215	1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6930404	0.86[EUR][1000 genomes]
rs6931802	1.00[CHB][hapmap]
rs6933721	1.00[ASW][hapmap];0.89[MKK][hapmap]
rs7749040	1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7766829	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs9373387	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs9376739	1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs9376743	1.00[CHB][hapmap]
rs9376745	1.00[CHB][hapmap]
rs9403480	0.86[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.91[AFR][1000 genomes];0.86[EUR][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	nsv981344	chr6:143566840-143579617	Strong transcription Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9496542	PLAGL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143527400-143578800	Weak transcription	Brain Hippocampus Middle	brain
2	chr6:143545400-143588800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:143546000-143576200	Weak transcription	HepG2	liver
4	chr6:143546200-143571200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:143550200-143570400	Weak transcription	Fetal Intestine Large	intestine
6	chr6:143554200-143581400	Weak transcription	Psoas Muscle	Psoas
7	chr6:143557600-143574000	Weak transcription	Left Ventricle	heart
8	chr6:143557600-143575200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:143562600-143574200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr6:143562600-143579000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:143563400-143577200	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:143563400-143579800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:143563600-143569600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:143563800-143569600	Weak transcription	Liver	Liver
15	chr6:143564200-143583000	Weak transcription	Pancreas	Pancrea
16	chr6:143565200-143573800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:143565200-143579400	Weak transcription	Ovary	ovary
18	chr6:143565600-143570400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:143565600-143578200	Weak transcription	Esophagus	oesophagus
20	chr6:143566200-143570200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:143566200-143574600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr6:143567600-143571200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:143568000-143569600	Enhancers	Aorta	Aorta
24	chr6:143568000-143578000	Weak transcription	K562	blood
25	chr6:143568200-143571000	Weak transcription	Fetal Intestine Small	intestine
26	chr6:143568600-143571400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr6:143569000-143592000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:143569200-143586600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr6:143569400-143570000	Enhancers	NHEK	skin

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