Variant report

Variant	rs17412941
Chromosome Location	chr9:71978004-71978005
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12003507	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12551899	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284247	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13284677	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13285975	0.88[ASN][1000 genomes]
rs13290881	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13291679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13296504	0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs13297121	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.85[ASN][1000 genomes]
rs13298045	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13300133	0.88[ASN][1000 genomes]
rs1855529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253778	0.82[JPT][hapmap];0.88[YRI][hapmap]
rs34133536	0.87[ASN][1000 genomes]
rs34295676	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34672585	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4307408	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4351475	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs4554547	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4744884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744885	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744893	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs60284429	0.88[ASN][1000 genomes]
rs7028920	0.91[JPT][hapmap]
rs7033124	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7853058	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7855000	0.87[ASN][1000 genomes]
rs7867609	0.91[CEU][hapmap];0.88[ASN][1000 genomes]
rs867365	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs867366	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv893428	chr9:71926658-72027641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv893429	chr9:71961923-72047337	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv893430	chr9:71968730-72036369	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17412941	CSGALNACT2	trans	cerebellum	SCAN
rs17412941	C9orf57	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71955400-71981800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:71962200-71994200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:71963200-71991800	Weak transcription	Pancreas	Pancrea
4	chr9:71972600-71978400	Weak transcription	Right Ventricle	heart
5	chr9:71972600-71980800	Weak transcription	Aorta	Aorta
6	chr9:71972600-71991800	Weak transcription	Right Atrium	heart
7	chr9:71972800-71991400	Weak transcription	Fetal Muscle Leg	muscle
8	chr9:71973000-71986200	Weak transcription	Stomach Mucosa	stomach
9	chr9:71973200-71979600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr9:71974800-71981600	Enhancers	Fetal Heart	heart
11	chr9:71974800-71982000	Weak transcription	Ovary	ovary
12	chr9:71976600-71981000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr9:71976600-71981200	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr9:71977000-71980600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr9:71977400-71992400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:71977600-71978800	Enhancers	Psoas Muscle	Psoas
17	chr9:71978000-71978600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr9:71978000-71978600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr9:71978000-71978800	Enhancers	Gastric	stomach
20	chr9:71978000-71978800	Enhancers	Left Ventricle	heart

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