Variant report

Variant	rs6559841
Chromosome Location	chr9:72508302-72508303
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10115144	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117766	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10122385	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1027288	0.95[ASN][1000 genomes]
rs10780684	0.80[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780685	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780686	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868224	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868225	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868227	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868234	0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1119563	0.95[ASN][1000 genomes]
rs1119564	0.95[ASN][1000 genomes]
rs1389123	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1389124	0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1389126	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1493055	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1586915	0.95[ASN][1000 genomes]
rs1826476	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1873823	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1873824	1.00[ASW][hapmap];0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1907960	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1907962	0.82[ASN][1000 genomes]
rs2035920	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2035921	0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2101686	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4237236	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4258059	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4363263	0.96[CEU][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4381006	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4381007	0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4407955	0.95[ASN][1000 genomes]
rs4475565	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4548246	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4584204	0.95[ASN][1000 genomes]
rs4744577	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744578	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744944	0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4744945	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744946	0.95[ASN][1000 genomes]
rs4744950	0.95[ASN][1000 genomes]
rs4744951	0.95[ASN][1000 genomes]
rs4744952	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55816194	0.95[ASN][1000 genomes]
rs6559830	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6559831	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6559835	0.95[ASN][1000 genomes]
rs6559842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6559843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7021905	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022703	0.95[ASN][1000 genomes]
rs7025411	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026857	0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7028323	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7042001	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7043409	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7043623	0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7045208	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047265	0.95[ASN][1000 genomes]
rs7465920	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs766003	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868466	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875361	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9285051	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990865	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050920	chr9:72345297-72579301	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv831611	chr9:72361905-72512134	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv831612	chr9:72473778-72634253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv471310	chr9:72479046-72508302	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv614580	chr9:72479046-72508302	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv466416	chr9:72479046-72513240	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv614581	chr9:72479046-72513240	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv893439	chr9:72500956-72568962	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6559841	C9orf135	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72500800-72509400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr9:72500800-72512800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr9:72501000-72509400	Weak transcription	Osteobl	bone
4	chr9:72501200-72509600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr9:72501200-72512600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:72501600-72509400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:72501800-72513000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:72502800-72512600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:72502800-72512600	Weak transcription	HMEC	breast
10	chr9:72504600-72509600	Weak transcription	A549	lung
11	chr9:72506200-72508400	Enhancers	Fetal Heart	heart
12	chr9:72507400-72508800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr9:72507800-72509000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:72508200-72508600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr9:72508200-72509000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:72508200-72509400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:72508200-72509600	Weak transcription	Right Ventricle	heart
18	chr9:72508200-72512600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr9:72508200-72512600	Weak transcription	Brain Inferior Temporal Lobe	brain

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