Variant report

Variant	rs11659091
Chromosome Location	chr17:67109662-67109663
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:67105618..67107692-chr17:67108283..67110713,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1011789	0.88[CHB][hapmap];0.91[CHD][hapmap]
rs1024598	0.88[CHB][hapmap];0.91[CHD][hapmap]
rs11077403	0.88[CHB][hapmap];0.91[CHD][hapmap]
rs11077942	0.92[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11652530	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs11654430	0.81[ASN][1000 genomes]
rs11654867	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11655912	0.87[CHB][hapmap]
rs11657954	0.85[EUR][1000 genomes]
rs11659119	0.88[CHB][hapmap]
rs12453921	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12939282	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs12942011	0.86[EUR][1000 genomes]
rs12943387	0.88[CHB][hapmap]
rs12950143	0.87[CHB][hapmap]
rs1558167	0.88[CHB][hapmap]
rs1974575	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1974578	0.81[ASN][1000 genomes]
rs2041171	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs2098034	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2302132	0.92[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs2302133	0.92[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs2302134	0.92[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs2302290	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2364315	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2364991	0.87[CHB][hapmap];0.91[CHD][hapmap]
rs2364992	0.88[CHB][hapmap];0.91[CHD][hapmap]
rs3744489	0.81[TSI][hapmap]
rs4141177	0.81[GIH][hapmap]
rs4968833	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4968842	0.81[ASN][1000 genomes]
rs4968995	0.83[EUR][1000 genomes]
rs5025273	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs721813	0.85[CHB][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs7221183	0.88[CHB][hapmap]
rs740517	0.89[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs7504026	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs763920	0.96[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs8064583	0.88[CHB][hapmap];0.91[CHD][hapmap]
rs8067584	0.88[CHB][hapmap];0.80[YRI][hapmap]
rs8069791	0.81[ASN][1000 genomes]
rs8071373	0.88[CHB][hapmap];0.91[CHD][hapmap];0.80[MKK][hapmap]
rs8071611	0.85[CHB][hapmap];0.90[CHD][hapmap];0.80[MKK][hapmap];0.81[ASN][1000 genomes]
rs8073982	0.87[CHB][hapmap]
rs8080693	0.88[CHB][hapmap];0.91[CHD][hapmap]
rs9282552	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9709278	0.81[ASN][1000 genomes]
rs981453	0.88[CHB][hapmap];0.91[CHD][hapmap];0.81[MKK][hapmap]
rs9894644	0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs9909216	0.88[CHB][hapmap];0.91[CHD][hapmap]
rs9914684	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833526	chr17:66980758-67137034	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv908705	chr17:67061898-67112456	Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	esv1850212	chr17:67081732-67117428	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
6	nsv470598	chr17:67081830-67212595	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11659091	ABCA9	cis	parietal	SCAN
rs11659091	CD79B	cis	cerebellum	SCAN
rs11659091	ABCA6	cis	parietal	SCAN
rs11659091	CACNG5	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67067200-67111600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr17:67076800-67109800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr17:67077800-67137800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr17:67079400-67112200	Strong transcription	Liver	Liver
5	chr17:67079400-67112600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr17:67079400-67117600	Weak transcription	Esophagus	oesophagus
7	chr17:67079600-67114200	Weak transcription	NHDF-Ad	bronchial
8	chr17:67080800-67112000	Weak transcription	Brain Substantia Nigra	brain
9	chr17:67081400-67118600	Weak transcription	Right Ventricle	heart
10	chr17:67082200-67114400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr17:67087000-67114600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:67087000-67130400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr17:67090400-67110000	Strong transcription	Adipose Nuclei	Adipose
14	chr17:67091200-67131400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr17:67091600-67130000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr17:67092200-67137600	Weak transcription	Brain Anterior Caudate	brain
17	chr17:67095800-67131000	Weak transcription	Fetal Muscle Leg	muscle
18	chr17:67096200-67143400	Weak transcription	Psoas Muscle	Psoas
19	chr17:67096400-67134000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr17:67097000-67133800	Weak transcription	Colon Smooth Muscle	Colon
21	chr17:67099000-67131600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr17:67101200-67110000	Weak transcription	Gastric	stomach
23	chr17:67101200-67143400	Weak transcription	Pancreas	Pancrea
24	chr17:67102000-67111200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr17:67102600-67111400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr17:67103200-67113400	Strong transcription	Fetal Lung	lung
27	chr17:67104800-67114600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr17:67106400-67131400	Weak transcription	Left Ventricle	heart
29	chr17:67108000-67117400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr17:67108400-67110800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr17:67108400-67114200	Weak transcription	Ovary	ovary
32	chr17:67108800-67111200	Weak transcription	Lung	lung
33	chr17:67109200-67109800	ZNF genes & repeats	GM12878-XiMat	blood
34	chr17:67109400-67112000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr17:67109400-67114400	Weak transcription	HUVEC	blood vessel
36	chr17:67109600-67109800	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr17:67109600-67110800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr17:67109600-67129200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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