Variant report

Variant	rs6078190
Chromosome Location	chr20:11428113-11428114
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11700189	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2207906	0.95[ASN][1000 genomes]
rs2207910	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2207911	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2423554	0.94[ASN][1000 genomes]
rs2876228	0.82[ASN][1000 genomes]
rs6040739	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6074301	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6078168	0.81[ASN][1000 genomes]
rs6078204	0.95[ASN][1000 genomes]
rs6104763	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6108906	0.86[JPT][hapmap]
rs6108988	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6108990	0.98[ASN][1000 genomes]
rs6131222	0.95[ASN][1000 genomes]
rs6134272	0.94[ASN][1000 genomes]
rs6134277	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs722568	1.00[MKK][hapmap]
rs728487	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8123803	0.95[ASN][1000 genomes]
rs973970	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065969	chr20:10850562-11464172	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv544181	chr20:10850562-11464172	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv432099	chr20:11371093-11476900	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1058734	chr20:11389232-11479953	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv522929	chr20:11411026-11516418	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6078190	PAK7	cis	parietal	SCAN
rs6078190	SNAP25	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11417000-11432200	Weak transcription	A549	lung
2	chr20:11423800-11429800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr20:11423800-11432400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr20:11424600-11428200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr20:11424600-11428400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:11424800-11428200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr20:11424800-11428200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr20:11424800-11428200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr20:11424800-11428200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr20:11424800-11432400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr20:11425000-11432200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr20:11425400-11428200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr20:11426200-11428400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr20:11426400-11432200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr20:11426600-11432200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr20:11426800-11428200	Weak transcription	HSMMtube	muscle
17	chr20:11426800-11432200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr20:11427200-11432200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr20:11427200-11432400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr20:11427200-11432400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr20:11427600-11429400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr20:11427800-11428800	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr20:11427800-11429000	Enhancers	H1 Cell Line	embryonic stem cell
24	chr20:11428000-11428200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr20:11428000-11428400	Enhancers	Psoas Muscle	Psoas
26	chr20:11428000-11428800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr20:11428000-11428800	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr20:11428000-11428800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr20:11428000-11428800	Enhancers	Esophagus	oesophagus
30	chr20:11428000-11428800	Enhancers	Fetal Muscle Leg	muscle
31	chr20:11428000-11429400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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