Variant report

Variant	rs36161
Chromosome Location	chr3:134656289-134656290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10935143	0.80[TSI][hapmap]
rs11707505	0.80[TSI][hapmap]
rs1457563	1.00[JPT][hapmap]
rs185257	0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs187587	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36160	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36165	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36167	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36168	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36169	0.84[CEU][hapmap];0.90[CHB][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36170	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36171	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36172	0.85[CEU][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36174	1.00[MEX][hapmap];0.80[AMR][1000 genomes]
rs36176	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36177	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36178	0.85[CEU][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36179	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36180	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36181	0.95[EUR][1000 genomes]
rs36182	0.85[CEU][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs36183	0.84[CEU][hapmap];0.94[EUR][1000 genomes]
rs36184	0.85[CEU][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs36185	0.84[CEU][hapmap];0.94[EUR][1000 genomes]
rs36186	0.81[CEU][hapmap];0.93[EUR][1000 genomes]
rs39701	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs39702	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs39703	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs39704	0.85[CEU][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs40157	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs40437	0.85[CEU][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs40438	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs42883	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs43208	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4955459	0.80[TSI][hapmap]
rs4955520	0.80[TSI][hapmap]
rs4955522	0.80[TSI][hapmap]
rs4955524	0.80[TSI][hapmap]
rs4955528	0.87[EUR][1000 genomes]
rs504033	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6763913	0.82[CHB][hapmap]
rs6795875	1.00[JPT][hapmap]
rs680054	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs972234	0.80[TSI][hapmap]
rs975149	0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs9815290	0.80[TSI][hapmap]
rs9819131	0.82[CHB][hapmap];0.91[EUR][1000 genomes]
rs9825380	0.80[TSI][hapmap]
rs9856814	0.85[TSI][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009634	chr3:134543259-134820208	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv536720	chr3:134543259-134820208	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1000277	chr3:134546080-134970837	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs36161	STAG1	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134644600-134656400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:134650600-134660600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:134653200-134657600	Enhancers	Brain Anterior Caudate	brain
4	chr3:134653400-134657200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:134653800-134659000	Enhancers	Brain Germinal Matrix	brain
6	chr3:134654200-134657400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:134654400-134656400	Weak transcription	Right Atrium	heart
8	chr3:134654600-134658200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:134654800-134657200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:134654800-134658800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:134655000-134659400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:134655200-134657200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:134655400-134657000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:134655600-134656600	Enhancers	GM12878-XiMat	blood
15	chr3:134655600-134657000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr3:134655600-134658400	Enhancers	H1 Cell Line	embryonic stem cell
17	chr3:134655800-134656400	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr3:134655800-134656400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:134655800-134657400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr3:134655800-134658000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr3:134655800-134658200	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr3:134655800-134658200	Enhancers	Fetal Brain Female	brain
23	chr3:134655800-134658600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:134655800-134658600	Enhancers	Fetal Brain Male	brain
25	chr3:134656000-134656600	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr3:134656000-134657400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr3:134656200-134656400	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr3:134656200-134656400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:134656200-134656600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:134656200-134656600	Enhancers	Adipose Nuclei	Adipose
31	chr3:134656200-134656600	Enhancers	Fetal Muscle Leg	muscle
32	chr3:134656200-134656600	Enhancers	Fetal Stomach	stomach
33	chr3:134656200-134656600	Enhancers	Left Ventricle	heart
34	chr3:134656200-134656800	Enhancers	Fetal Muscle Trunk	muscle
35	chr3:134656200-134657000	Enhancers	Brain Hippocampus Middle	brain
36	chr3:134656200-134657800	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr3:134656200-134658000	Enhancers	HUES48 Cell Line	embryonic stem cell

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