Variant report

Variant	rs394488
Chromosome Location	chr9:101469448-101469449
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101298822..101299808-chr9:101469168..101470098,4	K562	blood:
2	chr9:101469417..101470003-chr9:101537901..101538481,2	K562	blood:
3	chr9:101455554..101459399-chr9:101467510..101471263,4	MCF-7	breast:
4	chr9:100836437..100837120-chr9:101469356..101469982,2	K562	blood:
5	chr9:100967716..100968659-chr9:101469208..101469729,2	K562	blood:
6	chr9:101462868..101464769-chr9:101469228..101471376,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000095380	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs186808	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2095079	0.80[ASN][1000 genomes]
rs337525	0.83[ASN][1000 genomes]
rs337526	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs337528	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs337530	0.84[ASN][1000 genomes]
rs337531	0.84[ASN][1000 genomes]
rs337533	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs337534	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs337535	0.84[ASN][1000 genomes]
rs337536	0.84[ASN][1000 genomes]
rs337537	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs337538	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337544	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337545	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337546	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs337547	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337548	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs337550	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs337551	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs337552	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs337553	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs337556	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs337558	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337559	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3808896	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs405430	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs415902	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4517239	0.94[ASN][1000 genomes]
rs4743266	0.89[ASN][1000 genomes]
rs509747	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs516930	0.81[ASN][1000 genomes]
rs529278	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570138	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478811	0.84[AMR][1000 genomes];0.80[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	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv893614	chr9:101340316-101671634	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv893615	chr9:101356515-101678036	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv893616	chr9:101371017-101472921	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv825007	chr9:101467848-101476292	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3338088	chr9:101469131-101473529	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs394488	ANKS6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101468800-101469600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr9:101468800-101469800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
3	chr9:101468800-101469800	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr9:101469000-101469600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
5	chr9:101469000-101469600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
6	chr9:101469000-101469800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
7	chr9:101469000-101469800	Bivalent Enhancer	Fetal Stomach	stomach
8	chr9:101469000-101469800	Bivalent Enhancer	Ovary	ovary
9	chr9:101469000-101469800	Bivalent Enhancer	NHDF-Ad	bronchial
10	chr9:101469000-101470000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
11	chr9:101469000-101470000	Bivalent Enhancer	Spleen	Spleen
12	chr9:101469000-101470600	Flanking Active TSS	HUVEC	blood vessel
13	chr9:101469000-101470800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr9:101469000-101471000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr9:101469000-101471000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:101469000-101471800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
17	chr9:101469200-101469600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
18	chr9:101469200-101469600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
19	chr9:101469200-101469600	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:101469200-101469600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:101469200-101469600	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:101469200-101469600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr9:101469200-101469600	Bivalent Enhancer	Right Ventricle	heart
24	chr9:101469200-101469600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
25	chr9:101469200-101469600	Enhancers	K562	blood
26	chr9:101469200-101469800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr9:101469200-101469800	Bivalent Enhancer	HSMMtube	muscle
28	chr9:101469200-101470200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:101469200-101470200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr9:101469200-101470200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:101469200-101470200	Bivalent/Poised TSS	NHLF	lung
32	chr9:101469200-101470400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:101469200-101470400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
34	chr9:101469200-101470400	Bivalent Enhancer	Left Ventricle	heart
35	chr9:101469200-101470800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
36	chr9:101469200-101470800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
37	chr9:101469200-101470800	Bivalent/Poised TSS	Brain Substantia Nigra	brain
38	chr9:101469200-101470800	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr9:101469200-101470800	Bivalent Enhancer	Placenta	Placenta
40	chr9:101469200-101470800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
41	chr9:101469200-101471000	Bivalent Enhancer	HMEC	breast
42	chr9:101469200-101471800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
43	chr9:101469200-101471800	Enhancers	Liver	Liver
44	chr9:101469200-101472000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
45	chr9:101469200-101472000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
46	chr9:101469200-101472000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
47	chr9:101469200-101472000	Active TSS	Brain Angular Gyrus	brain
48	chr9:101469200-101472200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
49	chr9:101469400-101469600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
50	chr9:101469400-101469600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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