Variant report

Variant	rs10935417
Chromosome Location	chr3:140785834-140785835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11928846	0.84[CEU][hapmap]
rs12494997	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1365630	0.92[CEU][hapmap];0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs1426962	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1426963	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1559896	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs4683547	0.83[CEU][hapmap]
rs59279694	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6439977	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6793789	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6804474	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7622090	1.00[CEU][hapmap];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7639594	0.81[EUR][1000 genomes]
rs890528	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs890529	0.81[ASN][1000 genomes]
rs919157	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9817298	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9817591	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9823283	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9823690	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9842086	0.92[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.96[TSI][hapmap]
rs9844927	0.82[EUR][1000 genomes]
rs9882989	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][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	nsv432488	chr3:140752302-140790302	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10935417	BPESC1	cis	cerebellum	SCAN
rs10935417	SLC9A9	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140776000-140787600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:140776600-140787200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:140777400-140795000	Weak transcription	Fetal Brain Female	brain
4	chr3:140777600-140789600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:140779400-140788800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:140779600-140788200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:140782800-140787400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:140782800-140787800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:140782800-140789200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:140783000-140788000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:140783200-140786000	Weak transcription	Thymus	Thymus
12	chr3:140783600-140794200	Weak transcription	Fetal Kidney	kidney
13	chr3:140783800-140788200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:140784400-140788400	Strong transcription	Dnd41	blood
15	chr3:140784600-140786400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:140784800-140786000	Strong transcription	Fetal Stomach	stomach
17	chr3:140784800-140787200	Genic enhancers	Fetal Muscle Leg	muscle
18	chr3:140784800-140787800	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:140785200-140786600	Strong transcription	Brain Germinal Matrix	brain
20	chr3:140785400-140786000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:140785400-140786400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:140785400-140790000	Weak transcription	Right Ventricle	heart
23	chr3:140785600-140787800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:140785600-140788200	Enhancers	Pancreas	Pancrea
25	chr3:140785800-140786000	Weak transcription	Aorta	Aorta
26	chr3:140785800-140786200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr3:140785800-140786400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:140785800-140786400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr3:140785800-140787200	Enhancers	Fetal Lung	lung
30	chr3:140785800-140787600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:140785800-140795000	Enhancers	Fetal Heart	heart
32	chr3:140785800-140795000	Weak transcription	Lung	lung

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