Variant report

Variant	rs9366911
Chromosome Location	chr6:36589340-36589341
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36561436..36563651-chr6:36588757..36591345,2	MCF-7	breast:
2	chr6:36589213..36595227-chr6:36645571..36651666,9	K562	blood:
3	chr6:36581224..36597272-chr6:36642199..36659412,120	MCF-7	breast:
4	chr6:36581748..36603537-chr6:36641861..36652365,77	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112081	Chromatin interaction
ENSG00000124762	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10214849	1.00[CEU][hapmap];0.95[GIH][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs10223366	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10807169	0.81[EUR][1000 genomes]
rs10947613	0.84[CEU][hapmap];0.95[GIH][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes]
rs11756969	0.85[CEU][hapmap]
rs12153820	0.81[EUR][1000 genomes]
rs12197590	0.82[EUR][1000 genomes]
rs1406945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1812018	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs1812019	0.81[EUR][1000 genomes]
rs1812020	0.80[EUR][1000 genomes]
rs2145048	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4713987	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713988	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56144242	0.80[EUR][1000 genomes]
rs60627328	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61211228	0.81[EUR][1000 genomes]
rs671516	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6937430	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs73410251	0.92[EUR][1000 genomes]
rs7741888	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7755461	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs7759546	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7759778	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7759933	0.81[EUR][1000 genomes]
rs7760766	0.81[EUR][1000 genomes]
rs7767296	0.81[EUR][1000 genomes]
rs7771547	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9296192	0.86[EUR][1000 genomes]
rs9357217	0.81[EUR][1000 genomes]
rs9357219	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9366907	0.81[EUR][1000 genomes]
rs9366908	0.81[EUR][1000 genomes]
rs9366909	0.81[EUR][1000 genomes]
rs9368938	0.81[EUR][1000 genomes]
rs9368940	0.81[EUR][1000 genomes]
rs9368942	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9380577	0.81[EUR][1000 genomes]
rs9380580	0.81[EUR][1000 genomes]
rs9380582	0.81[EUR][1000 genomes]
rs9394362	0.81[EUR][1000 genomes]
rs9394363	0.85[CEU][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	nsv885806	chr6:36349890-36621178	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
2	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9366911	ASAP2	trans	brain	seeQTL
rs9366911	CPNE5	cis	cerebellum	SCAN
rs9366911	RPS6KB1	trans	brain	seeQTL
rs9366911	SRPK1	cis	brain	seeQTL
rs9366911	MEGF9	trans	cerebellum	SCAN
rs9366911	PXT1	cis	lymphoblastoid	seeQTL
rs9366911	LRFN2	cis	cerebellum	SCAN
rs9366911	TTC39C	trans	brain	seeQTL
rs9366911	GLO1	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36576200-36590800	Weak transcription	Right Atrium	heart
2	chr6:36577400-36595200	Weak transcription	Psoas Muscle	Psoas
3	chr6:36577800-36591000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:36577800-36595200	Weak transcription	Small Intestine	intestine
5	chr6:36580200-36590800	Weak transcription	NHLF	lung
6	chr6:36580200-36591000	Weak transcription	Ovary	ovary
7	chr6:36580200-36591000	Weak transcription	NH-A	brain
8	chr6:36580200-36599200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:36580400-36590800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:36580400-36591000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:36580400-36593000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:36581400-36590800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:36581400-36590800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:36581400-36591000	Weak transcription	Primary T cells from cord blood	blood
15	chr6:36581400-36591000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr6:36581400-36591000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr6:36581400-36591000	Weak transcription	Fetal Kidney	kidney
18	chr6:36581400-36591000	Weak transcription	Dnd41	blood
19	chr6:36581400-36604400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:36581600-36589600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:36581600-36590400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:36581600-36591000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr6:36581600-36591200	Weak transcription	Fetal Lung	lung
24	chr6:36581800-36590800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr6:36582000-36591200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:36582200-36595400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:36582800-36610800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:36583000-36590800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:36583400-36590800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr6:36583600-36590800	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr6:36583600-36591000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:36584600-36591400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:36584800-36591000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:36585000-36589400	Weak transcription	Brain Germinal Matrix	brain
35	chr6:36585200-36590200	Weak transcription	Adipose Nuclei	Adipose
36	chr6:36585200-36590600	Weak transcription	Colonic Mucosa	Colon
37	chr6:36585200-36590600	Weak transcription	Placenta	Placenta
38	chr6:36585200-36590800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr6:36585200-36590800	Weak transcription	Esophagus	oesophagus
40	chr6:36585200-36591000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr6:36585200-36591400	Weak transcription	Gastric	stomach
42	chr6:36585400-36590600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:36585400-36590600	Weak transcription	Fetal Intestine Large	intestine
44	chr6:36585400-36590800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr6:36585400-36590800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:36585400-36590800	Weak transcription	HSMMtube	muscle
47	chr6:36585400-36590800	Weak transcription	NHDF-Ad	bronchial
48	chr6:36585400-36591000	Weak transcription	Brain Substantia Nigra	brain
49	chr6:36585400-36591000	Weak transcription	Osteobl	bone
50	chr6:36585400-36592800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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