Variant report

Variant	rs9882989
Chromosome Location	chr3:140787552-140787553
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:140660042..140662305-chr3:140787345..140789644,2	K562	blood:
2	chr3:140785941..140788584-chr3:140792512..140794344,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114120	Chromatin interaction

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

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

rs_ID	r²[population]
rs10935417	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11928846	0.84[CEU][hapmap]
rs12494997	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1365630	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1426962	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1426963	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1559896	0.84[CEU][hapmap]
rs4683547	0.82[CEU][hapmap]
rs59279694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6439977	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6771494	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6793789	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6804474	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7622090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7639594	0.82[EUR][1000 genomes]
rs890528	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs919157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9817298	0.87[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9817591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9823283	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9823690	0.87[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9842086	0.92[CEU][hapmap];0.90[CHB][hapmap];0.96[TSI][hapmap]
rs9844927	0.81[EUR][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
rs9882989	BPESC1	cis	cerebellum	SCAN
rs9882989	SLC9A9	cis	parietal	SCAN

Chromatin state (count:28 , 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	chr3:140777400-140795000	Weak transcription	Fetal Brain Female	brain
3	chr3:140777600-140789600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:140779400-140788800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:140779600-140788200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:140782800-140787800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:140782800-140789200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:140783000-140788000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:140783600-140794200	Weak transcription	Fetal Kidney	kidney
10	chr3:140783800-140788200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:140784400-140788400	Strong transcription	Dnd41	blood
12	chr3:140784800-140787800	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:140785400-140790000	Weak transcription	Right Ventricle	heart
14	chr3:140785600-140787800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:140785600-140788200	Enhancers	Pancreas	Pancrea
16	chr3:140785800-140787600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:140785800-140795000	Enhancers	Fetal Heart	heart
18	chr3:140785800-140795000	Weak transcription	Lung	lung
19	chr3:140786000-140788000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:140786200-140794000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:140786400-140789600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:140786600-140789400	Weak transcription	Brain Germinal Matrix	brain
23	chr3:140786800-140787600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:140786800-140789600	Weak transcription	Fetal Stomach	stomach
25	chr3:140786800-140789800	Strong transcription	Fetal Muscle Trunk	muscle
26	chr3:140787200-140788000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:140787200-140788200	Strong transcription	Fetal Muscle Leg	muscle
28	chr3:140787200-140789800	Weak transcription	Fetal Lung	lung

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