Variant report

Variant	rs12352441
Chromosome Location	chr9:26962769-26962770
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	chr9:26945744..26947634-chr9:26962535..26964284,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137055	Chromatin interaction
ENSG00000096872	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10283643	1.00[CHB][hapmap]
rs10511793	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[ASN][1000 genomes]
rs10812492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10812500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10967593	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10967594	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[ASN][1000 genomes]
rs10967624	1.00[CHB][hapmap];0.87[MKK][hapmap]
rs10967625	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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]
rs10967634	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[MKK][hapmap]
rs10967639	1.00[CHB][hapmap]
rs10967640	1.00[CHB][hapmap]
rs1161603	1.00[CHB][hapmap]
rs11788136	1.00[CHB][hapmap]
rs12001845	1.00[CHB][hapmap]
rs12002260	0.95[ASN][1000 genomes]
rs12003612	1.00[CHD][hapmap]
rs12005388	1.00[CHB][hapmap]
rs12337860	1.00[CHB][hapmap]
rs12338678	1.00[CHB][hapmap]
rs12339162	1.00[CHB][hapmap]
rs12340500	1.00[CHB][hapmap]
rs12342005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12343345	1.00[CHB][hapmap]
rs12345094	1.00[CHB][hapmap]
rs12349359	1.00[CHB][hapmap]
rs12352603	1.00[CHB][hapmap]
rs12352631	1.00[CHB][hapmap]
rs12554485	1.00[CHB][hapmap]
rs13293051	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs16910888	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[ASN][1000 genomes]
rs16910895	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16911083	1.00[CHB][hapmap]
rs17694121	1.00[CHB][hapmap]
rs17694140	1.00[CHB][hapmap]
rs17694300	1.00[CHB][hapmap]
rs17694306	1.00[CHB][hapmap]
rs17694549	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17694796	1.00[CHB][hapmap]
rs17755887	1.00[CHB][hapmap]
rs17755911	1.00[CHB][hapmap]
rs17756599	1.00[CHB][hapmap]
rs17756667	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17756685	1.00[CHB][hapmap]
rs2027124	1.00[CHB][hapmap]
rs2152063	1.00[CHB][hapmap]
rs2991949	1.00[CHB][hapmap]
rs3429	1.00[CHB][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs57770546	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs59274950	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs596427	1.00[CHB][hapmap]
rs615532	1.00[CHB][hapmap]
rs62542667	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62542672	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62542704	0.80[EUR][1000 genomes]
rs62544439	0.95[ASN][1000 genomes]
rs62544443	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62544450	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62544451	0.86[EUR][1000 genomes]
rs62544452	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6475948	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6475959	1.00[CHB][hapmap]
rs6475963	1.00[CHB][hapmap]
rs6475966	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6475968	1.00[CHB][hapmap]
rs7023230	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7035755	0.86[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7037860	1.00[CHB][hapmap]
rs7039400	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7040516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7040772	1.00[CHB][hapmap]
rs7042003	1.00[CHB][hapmap]
rs7042119	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7044842	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7045881	0.86[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73436047	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73438223	0.80[EUR][1000 genomes]
rs7847280	1.00[CHB][hapmap]
rs7851339	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7851423	0.86[AMR][1000 genomes]
rs7851582	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7854048	1.00[CHB][hapmap]
rs7857669	0.80[TSI][hapmap]
rs7871097	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[ASN][1000 genomes]
rs7871178	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7871286	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[ASN][1000 genomes]
rs7872881	0.82[EUR][1000 genomes]
rs7873019	1.00[CHB][hapmap]
rs7873161	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7873329	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528614	chr9:26893662-27074233	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv517269	chr9:26945976-27137242	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv892862	chr9:26956663-27190655	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12352441	C9orf82	cis	parietal	SCAN
rs12352441	IFT74	cis	lymphoblastoid	seeQTL
rs12352441	C9orf82	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26957000-26973800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr9:26957000-26980800	Weak transcription	Lung	lung
3	chr9:26957000-26983200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:26957000-26984400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr9:26957000-27024000	Weak transcription	Esophagus	oesophagus
6	chr9:26957200-26976000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:26957200-26980800	Weak transcription	Fetal Intestine Large	intestine
8	chr9:26957200-26980800	Weak transcription	Fetal Stomach	stomach
9	chr9:26957200-26982600	Weak transcription	Fetal Muscle Leg	muscle
10	chr9:26957200-26982600	Weak transcription	Left Ventricle	heart
11	chr9:26957200-26983200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr9:26957200-26983200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr9:26957200-26984400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr9:26957200-26984400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr9:26957200-26984600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr9:26957200-26984800	Weak transcription	Primary B cells from cord blood	blood
17	chr9:26957200-26984800	Weak transcription	Fetal Thymus	thymus
18	chr9:26957200-27026600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr9:26957200-27040000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr9:26957400-26963800	Weak transcription	NHLF	lung
21	chr9:26957400-26964800	Weak transcription	Primary T cells from cord blood	blood
22	chr9:26957400-26974800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr9:26957400-26978200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr9:26957400-26980800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr9:26957400-26982800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr9:26957400-26983200	Weak transcription	Brain Anterior Caudate	brain
27	chr9:26957400-26983400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr9:26957400-26984600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr9:26957600-26965800	Weak transcription	Fetal Brain Female	brain
30	chr9:26957600-26975200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:26957600-26979400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:26957600-26982800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:26957600-26983200	Weak transcription	Fetal Kidney	kidney
34	chr9:26957600-26983400	Weak transcription	Brain Angular Gyrus	brain
35	chr9:26957600-26984800	Weak transcription	Brain Hippocampus Middle	brain
36	chr9:26957800-26963800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr9:26957800-26965000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr9:26957800-26974600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr9:26957800-26975600	Weak transcription	Fetal Intestine Small	intestine
40	chr9:26957800-26976600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr9:26957800-26984600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr9:26958400-26965000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr9:26958600-26965200	Weak transcription	Dnd41	blood
44	chr9:26958600-26967600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr9:26958600-26981000	Weak transcription	Ovary	ovary
46	chr9:26960000-26965000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr9:26960000-26971600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:26960000-26976200	Weak transcription	NHEK	skin
49	chr9:26960000-26976600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr9:26961800-26964000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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