Variant report

Variant	rs10746594
Chromosome Location	chr9:71984887-71984888
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10116389	1.00[ASW][hapmap];0.87[CEU][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.93[MKK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs10217407	0.85[JPT][hapmap]
rs10283713	0.85[JPT][hapmap]
rs10283788	0.85[JPT][hapmap]
rs1029064	0.84[JPT][hapmap]
rs1029065	0.85[JPT][hapmap]
rs10746613	0.81[AFR][1000 genomes]
rs10780360	0.85[JPT][hapmap]
rs10780361	0.85[JPT][hapmap]
rs10867414	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10867423	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10867647	0.85[JPT][hapmap]
rs10867671	0.85[JPT][hapmap]
rs10867672	0.85[JPT][hapmap]
rs1113067	0.85[JPT][hapmap]
rs11138927	0.84[JPT][hapmap]
rs11138980	0.85[JPT][hapmap]
rs11138986	0.82[JPT][hapmap]
rs11139043	0.85[JPT][hapmap]
rs11139050	0.85[JPT][hapmap]
rs11139160	0.84[JPT][hapmap]
rs11139181	0.85[JPT][hapmap]
rs11788742	0.85[JPT][hapmap]
rs12235168	0.85[JPT][hapmap]
rs12238067	0.85[JPT][hapmap]
rs12344522	0.82[JPT][hapmap]
rs12348063	0.82[JPT][hapmap]
rs12379338	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1331979	0.82[JPT][hapmap]
rs1334312	0.94[CEU][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1929896	0.93[CEU][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs2297421	0.84[JPT][hapmap]
rs2309431	1.00[ASW][hapmap];0.87[CEU][hapmap];0.87[LWK][hapmap];0.87[MKK][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs2777866	0.87[CEU][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs2777878	0.87[CEU][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs2781521	0.87[CEU][hapmap];0.84[YRI][hapmap]
rs2781522	0.87[CEU][hapmap];0.84[YRI][hapmap]
rs3858105	0.94[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs3897966	0.85[JPT][hapmap]
rs3934600	0.87[CEU][hapmap];0.86[GIH][hapmap]
rs4237233	1.00[ASW][hapmap];0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[YRI][hapmap]
rs4237234	1.00[ASW][hapmap];0.87[CEU][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs4483220	0.87[CEU][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs4484762	0.87[CEU][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs4744570	0.82[JPT][hapmap]
rs4744886	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4744894	1.00[ASW][hapmap];0.87[CEU][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs4744904	0.85[JPT][hapmap]
rs4744910	0.85[JPT][hapmap]
rs4744911	0.85[JPT][hapmap]
rs6559488	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6559489	0.94[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6559490	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6559498	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6559512	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs6559513	0.86[CEU][hapmap]
rs6559527	0.81[CEU][hapmap]
rs7019551	0.93[CEU][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7043451	0.84[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7044071	0.91[JPT][hapmap]
rs7046199	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7357615	0.85[JPT][hapmap]
rs7856778	0.87[CEU][hapmap];0.83[YRI][hapmap]
rs7866250	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10746594	C18orf16	trans	cerebellum	SCAN
rs10746594	TJP2	cis	cerebellum	SCAN
rs10746594	C9orf57	cis	cerebellum	SCAN
rs10746594	KLF9	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71962200-71994200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:71963200-71991800	Weak transcription	Pancreas	Pancrea
3	chr9:71972600-71991800	Weak transcription	Right Atrium	heart
4	chr9:71972800-71991400	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:71973000-71986200	Weak transcription	Stomach Mucosa	stomach
6	chr9:71977400-71992400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:71978600-71985200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:71978800-71987200	Weak transcription	Psoas Muscle	Psoas
9	chr9:71978800-71989200	Weak transcription	Right Ventricle	heart
10	chr9:71978800-71991600	Weak transcription	Left Ventricle	heart
11	chr9:71979000-72001800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr9:71982200-71985200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:71982200-71986400	Weak transcription	Ovary	ovary
14	chr9:71983400-72001800	Weak transcription	Brain Anterior Caudate	brain
15	chr9:71983600-71985200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr9:71984600-71985600	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr9:71984600-71985800	Enhancers	Fetal Heart	heart
18	chr9:71984600-71987000	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr9:71984800-71986200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:71984800-71986600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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