Variant report

Variant	rs919157
Chromosome Location	chr3:140782639-140782640
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXP2	chr3:140782635-140782903	SK-N-MC	brain:	n/a	n/a
2	EP300	chr3:140782466-140783293	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:140782511..140785350-chr3:140792921..140794807,2	K562	blood:

Variant related genes	Relation type
SPSB4	TF binding region

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

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

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

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
rs919157	SLC9A9	cis	parietal	SCAN
rs919157	BPESC1	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140775800-140784200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr3:140776000-140783400	Weak transcription	Right Atrium	heart
3	chr3:140776000-140787600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:140776600-140787200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:140777400-140795000	Weak transcription	Fetal Brain Female	brain
6	chr3:140777600-140782800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:140777600-140785200	Weak transcription	Brain Germinal Matrix	brain
8	chr3:140777600-140789600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:140777800-140782800	Weak transcription	Right Ventricle	heart
10	chr3:140778000-140784800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:140778400-140783000	Weak transcription	Fetal Stomach	stomach
12	chr3:140779000-140785400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:140779400-140785400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:140779400-140788800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:140779600-140788200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:140781800-140783800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:140782000-140783000	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr3:140782000-140783200	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr3:140782000-140784400	Enhancers	Fetal Lung	lung
20	chr3:140782000-140784600	Enhancers	Fetal Heart	heart
21	chr3:140782200-140782800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:140782200-140783200	Flanking Active TSS	Dnd41	blood
23	chr3:140782400-140782800	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr3:140782400-140783000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:140782400-140783200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:140782400-140783200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:140782400-140783200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr3:140782400-140784800	Enhancers	Fetal Muscle Leg	muscle
29	chr3:140782600-140782800	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr3:140782600-140782800	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr3:140782600-140782800	Enhancers	Psoas Muscle	Psoas
32	chr3:140782600-140783000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr3:140782600-140783000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:140782600-140783200	Enhancers	Primary T cells fromperipheralblood	blood
35	chr3:140782600-140783200	Enhancers	Fetal Thymus	thymus
36	chr3:140782600-140783200	Enhancers	Thymus	Thymus
37	chr3:140782600-140783600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:140782600-140783600	Enhancers	Fetal Kidney	kidney
39	chr3:140782600-140784200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:140782600-140784200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:140782600-140785200	Enhancers	Pancreas	Pancrea

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