Variant report

Variant	rs11936468
Chromosome Location	chr4:20548976-20548977
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	chr4:20423426..20426001-chr4:20546337..20549229,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10516358	0.88[CHD][hapmap]
rs1457919	0.90[JPT][hapmap]
rs1463463	0.89[CHB][hapmap];0.89[ASN][1000 genomes]
rs1870260	0.89[CHB][hapmap];0.92[CHD][hapmap];0.89[ASN][1000 genomes]
rs2168802	0.84[CHD][hapmap]
rs2290749	0.89[CHB][hapmap];0.96[CHD][hapmap];0.89[ASN][1000 genomes]
rs2290750	0.96[CHD][hapmap];0.82[ASN][1000 genomes]
rs2290751	0.92[CHD][hapmap];0.82[ASN][1000 genomes]
rs2292439	0.85[CHD][hapmap]
rs2446087	0.90[EUR][1000 genomes]
rs34337410	0.82[ASN][1000 genomes]
rs3775827	0.82[CHD][hapmap]
rs3886678	0.87[ASN][1000 genomes]
rs4697169	0.82[JPT][hapmap]
rs506358	0.88[CHD][hapmap];0.90[JPT][hapmap]
rs532992	0.80[EUR][1000 genomes]
rs571433	0.90[JPT][hapmap]
rs575088	0.82[JPT][hapmap]
rs587883	0.81[JPT][hapmap]
rs606524	0.86[CHB][hapmap];0.91[ASN][1000 genomes]
rs609535	0.87[MEX][hapmap];0.82[TSI][hapmap]
rs621806	0.93[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs636798	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs652756	0.80[EUR][1000 genomes]
rs6827219	0.81[CHB][hapmap]
rs6847226	0.89[CHB][hapmap];0.93[ASN][1000 genomes]
rs6853061	0.82[ASN][1000 genomes]
rs7666974	0.93[MEX][hapmap]
rs7692811	0.89[CHB][hapmap];0.96[CHD][hapmap];0.89[ASN][1000 genomes]
rs9992591	0.87[MEX][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	nsv829875	chr4:20502895-20680956	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	89 gene(s)	inside rSNPs	diseases
2	nsv999482	chr4:20546216-20563747	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1007227	chr4:20547578-20563930	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv516999	chr4:20548976-20565861	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11936468	PACRGL	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20492000-20599800	Weak transcription	Aorta	Aorta
2	chr4:20511800-20576200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:20519400-20571000	Weak transcription	Adipose Nuclei	Adipose
4	chr4:20524200-20555200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr4:20525200-20555400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:20530400-20555400	Weak transcription	NHEK	skin
7	chr4:20533000-20578000	Weak transcription	NHLF	lung
8	chr4:20533800-20576200	Weak transcription	Left Ventricle	heart
9	chr4:20534600-20552800	Weak transcription	Brain Anterior Caudate	brain
10	chr4:20534800-20576400	Weak transcription	Fetal Brain Male	brain
11	chr4:20535800-20593600	Weak transcription	Fetal Kidney	kidney
12	chr4:20536000-20552400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:20536000-20554800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:20536000-20555200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr4:20536600-20572200	Weak transcription	Placenta	Placenta
16	chr4:20536800-20618600	Weak transcription	Spleen	Spleen
17	chr4:20537800-20552600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:20537800-20552600	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:20537800-20552800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr4:20538000-20553200	Weak transcription	Fetal Stomach	stomach
21	chr4:20539000-20552800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:20541200-20552800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:20543600-20549600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:20543600-20549800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr4:20545000-20549800	Weak transcription	Osteobl	bone
26	chr4:20545000-20552600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:20546800-20550000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:20546800-20550600	Strong transcription	Fetal Lung	lung
29	chr4:20547000-20576000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:20547400-20550800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:20547800-20549800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:20548000-20550000	Weak transcription	NHDF-Ad	bronchial
33	chr4:20548600-20549200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:20548800-20549200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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