Variant report

Variant	rs6804474
Chromosome Location	chr3:140784435-140784436
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	chr3:140782511..140785350-chr3:140792921..140794807,2	K562	blood:

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

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

rs_ID	r²[population]
rs10935417	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11928846	0.84[CEU][hapmap]
rs12494997	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1365630	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs1426962	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1426963	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1559896	0.84[CEU][hapmap];0.80[TSI][hapmap]
rs4683547	0.83[CEU][hapmap]
rs59279694	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439977	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6771494	0.82[ASN][1000 genomes]
rs6793789	1.00[CEU][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7622090	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7639594	0.83[EUR][1000 genomes]
rs890528	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs890529	0.87[AFR][1000 genomes]
rs919157	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9817298	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9817591	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9823283	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9823690	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]
rs9842086	0.92[CEU][hapmap];0.84[CHB][hapmap];0.96[TSI][hapmap]
rs9882989	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]

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
rs6804474	BPESC1	cis	cerebellum	SCAN
rs6804474	SLC9A9	cis	parietal	SCAN

Chromatin state (count:34 , 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	chr3:140777600-140785200	Weak transcription	Brain Germinal Matrix	brain
5	chr3:140777600-140789600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:140778000-140784800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:140779000-140785400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:140779400-140785400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:140779400-140788800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:140779600-140788200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:140782000-140784600	Enhancers	Fetal Heart	heart
12	chr3:140782400-140784800	Enhancers	Fetal Muscle Leg	muscle
13	chr3:140782600-140785200	Enhancers	Pancreas	Pancrea
14	chr3:140782800-140784800	Enhancers	Fetal Muscle Trunk	muscle
15	chr3:140782800-140785400	Enhancers	Right Ventricle	heart
16	chr3:140782800-140787400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:140782800-140787800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:140782800-140789200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:140783000-140784600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:140783000-140785200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:140783000-140788000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:140783200-140784800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:140783200-140786000	Weak transcription	Thymus	Thymus
24	chr3:140783600-140784800	Weak transcription	Fetal Stomach	stomach
25	chr3:140783600-140794200	Weak transcription	Fetal Kidney	kidney
26	chr3:140783800-140788200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:140784200-140784800	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr3:140784200-140785000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:140784200-140785000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr3:140784200-140785200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:140784200-140785400	Weak transcription	Right Atrium	heart
32	chr3:140784400-140785800	Weak transcription	Fetal Lung	lung
33	chr3:140784400-140785800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:140784400-140788400	Strong transcription	Dnd41	blood

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