Variant report

Variant	rs1591421
Chromosome Location	chr9:117945427-117945428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10739433	0.86[JPT][hapmap]
rs10817722	0.85[JPT][hapmap]
rs10982546	0.83[MEX][hapmap]
rs13302198	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1335330	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs1335340	0.86[JPT][hapmap]
rs1335342	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1335343	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1335344	0.82[JPT][hapmap]
rs1335345	0.82[JPT][hapmap]
rs1335351	0.82[JPT][hapmap]
rs1414148	0.82[JPT][hapmap]
rs1537721	0.80[EUR][1000 genomes]
rs1537722	0.82[EUR][1000 genomes]
rs1537727	0.81[EUR][1000 genomes]
rs1537728	0.80[EUR][1000 genomes]
rs1855691	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2094941	0.81[EUR][1000 genomes]
rs4335203	0.82[CHD][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs4978623	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4978626	0.82[JPT][hapmap]
rs4979509	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4979510	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55991771	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56394382	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478147	0.86[JPT][hapmap]
rs6478148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478150	0.82[JPT][hapmap]
rs6478153	0.82[JPT][hapmap]
rs7027882	0.82[JPT][hapmap]
rs7044556	0.82[JPT][hapmap]
rs945258	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv893769	chr9:117936903-117985886	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1591421	TXN	cis	cerebellum	SCAN
rs1591421	C9orf80	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117930000-117964400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:117943200-117947000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr9:117944000-117947200	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr9:117944400-117946200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr9:117944400-117946200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr9:117944400-117946200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr9:117944400-117946200	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr9:117944400-117947000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:117944600-117946200	Enhancers	H1 Cell Line	embryonic stem cell
10	chr9:117944800-117946600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr9:117944800-117947000	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:117945200-117945600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:117945400-117945600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:117945400-117945600	Enhancers	Fetal Kidney	kidney
15	chr9:117945400-117946000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:117945400-117946200	Enhancers	H9 Cell Line	embryonic stem cell
17	chr9:117945400-117946200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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