Variant report

Variant	rs9823690
Chromosome Location	chr3:140790579-140790580
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:140785419..140788357-chr3:140788951..140791966,3	MCF-7	breast:
2	chr3:140789496..140791213-chr3:140794078..140795843,2	K562	blood:
3	chr3:140789863..140792661-chr3:140847892..140850124,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175093	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

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

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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9823690	BPESC1	cis	cerebellum	SCAN
rs9823690	SLC9A9	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140777400-140795000	Weak transcription	Fetal Brain Female	brain
2	chr3:140783600-140794200	Weak transcription	Fetal Kidney	kidney
3	chr3:140785800-140795000	Enhancers	Fetal Heart	heart
4	chr3:140785800-140795000	Weak transcription	Lung	lung
5	chr3:140786200-140794000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:140787800-140791200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:140788000-140791400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr3:140788000-140793000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:140788200-140791800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:140788200-140797200	Enhancers	H9 Cell Line	embryonic stem cell
11	chr3:140788600-140795000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:140788800-140791200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:140788800-140791600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr3:140789000-140797600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr3:140789200-140790600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr3:140789200-140791000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:140789400-140791400	Enhancers	Brain Germinal Matrix	brain
18	chr3:140789400-140795800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr3:140789600-140790800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr3:140789600-140791200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:140789600-140791400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:140789600-140791400	Genic enhancers	Fetal Muscle Leg	muscle
23	chr3:140789600-140791800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr3:140789600-140798000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:140789800-140790600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:140789800-140790600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:140789800-140790600	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr3:140789800-140790600	Enhancers	Fetal Brain Male	brain
29	chr3:140789800-140790600	Strong transcription	Dnd41	blood
30	chr3:140789800-140791000	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr3:140789800-140791200	Enhancers	Fetal Lung	lung
32	chr3:140789800-140791200	Enhancers	Pancreas	Pancrea
33	chr3:140789800-140791400	Genic enhancers	Fetal Muscle Trunk	muscle
34	chr3:140790000-140790800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:140790000-140791200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr3:140790200-140790800	Weak transcription	Right Ventricle	heart
37	chr3:140790200-140791000	Genic enhancers	Fetal Stomach	stomach
38	chr3:140790200-140795400	Weak transcription	Fetal Intestine Small	intestine
39	chr3:140790400-140790600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:140790400-140790800	Enhancers	Right Atrium	heart
41	chr3:140790400-140791000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:140790400-140791200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:140790400-140791800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell

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