Variant report

Variant	rs40437
Chromosome Location	chr3:134650932-134650933
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10935143	0.82[TSI][hapmap]
rs11707505	0.82[TSI][hapmap]
rs185257	0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs187587	1.00[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36160	0.92[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36161	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]
rs36165	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36167	0.96[CEU][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36168	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36169	0.92[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36170	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36171	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36172	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36174	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs36175	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs36176	1.00[CEU][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36177	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36178	1.00[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36179	1.00[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36180	0.95[CEU][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36181	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36182	1.00[CEU][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36183	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs36184	1.00[CEU][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36185	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36186	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36187	0.81[EUR][1000 genomes]
rs39701	1.00[CEU][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs39702	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs39703	1.00[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs39704	1.00[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs40157	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs42883	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs43208	0.81[AMR][1000 genomes]
rs4955459	0.82[TSI][hapmap]
rs4955520	0.82[TSI][hapmap]
rs4955522	0.82[TSI][hapmap]
rs4955524	0.82[TSI][hapmap]
rs4955527	0.80[TSI][hapmap]
rs4955528	0.87[EUR][1000 genomes]
rs504033	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6781640	0.80[TSI][hapmap]
rs680054	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7644369	0.82[TSI][hapmap]
rs936323	0.80[TSI][hapmap]
rs972234	0.82[TSI][hapmap]
rs975149	0.82[LWK][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs9815290	0.82[TSI][hapmap]
rs9819131	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs9825380	0.82[TSI][hapmap]
rs9856814	0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs9876803	0.82[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs40437	STAG1	cis	parietal	SCAN
rs40437	EPHB1	cis	multi-tissue	Pritchard
rs40437	DNAJC13	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134639400-134653800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr3:134642400-134653800	Weak transcription	Brain Germinal Matrix	brain
3	chr3:134644200-134654800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:134644600-134656400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:134649000-134656200	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:134649000-134656200	Weak transcription	Fetal Stomach	stomach
7	chr3:134649200-134651600	Enhancers	Rectal Smooth Muscle	rectum
8	chr3:134649200-134652400	Enhancers	Colon Smooth Muscle	Colon
9	chr3:134649600-134651000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:134649600-134651200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr3:134649800-134653400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:134650000-134651800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr3:134650200-134653200	Weak transcription	Brain Anterior Caudate	brain
14	chr3:134650400-134651200	Enhancers	Fetal Brain Male	brain
15	chr3:134650400-134651800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:134650400-134656000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr3:134650600-134652400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:134650600-134652600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:134650600-134653600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:134650600-134655600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:134650600-134655600	Weak transcription	GM12878-XiMat	blood
22	chr3:134650600-134660600	Weak transcription	H9 Cell Line	embryonic stem cell

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