Variant report

Variant	rs890528
Chromosome Location	chr3:140778763-140778764
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

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

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	esv3464316	chr3:140776527-140779000	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv3464317	chr3:140776527-140779000	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs890528	SLC9A9	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140772000-140779000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:140772000-140782600	Weak transcription	Psoas Muscle	Psoas
3	chr3:140772200-140779000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:140775200-140779000	Weak transcription	Fetal Lung	lung
5	chr3:140775800-140784200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:140776000-140779600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:140776000-140783400	Weak transcription	Right Atrium	heart
8	chr3:140776000-140787600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:140776400-140779000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:140776600-140779200	Enhancers	Pancreas	Pancrea
11	chr3:140776600-140787200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:140777200-140781200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:140777400-140779000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:140777400-140782600	Weak transcription	Fetal Kidney	kidney
15	chr3:140777400-140795000	Weak transcription	Fetal Brain Female	brain
16	chr3:140777600-140782800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:140777600-140785200	Weak transcription	Brain Germinal Matrix	brain
18	chr3:140777600-140789600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:140777800-140779000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
20	chr3:140777800-140782800	Weak transcription	Right Ventricle	heart
21	chr3:140778000-140780800	Weak transcription	Dnd41	blood
22	chr3:140778000-140784800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:140778400-140778800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:140778400-140782200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:140778400-140783000	Weak transcription	Fetal Stomach	stomach
26	chr3:140778600-140778800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:140778600-140778800	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:140778600-140779800	Enhancers	Fetal Heart	heart
29	chr3:140778600-140782600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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