Variant report

Variant	rs509747
Chromosome Location	chr9:101469934-101469935
allele	C/G
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	chr9:101462868..101464769-chr9:101469228..101471376,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000095380	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10512258	0.83[CEU][hapmap]
rs1571927	0.83[EUR][1000 genomes]
rs186808	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1930139	0.83[EUR][1000 genomes]
rs2225558	0.83[EUR][1000 genomes]
rs337526	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs337528	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs337529	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs337532	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs337533	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs337534	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs337537	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs337538	0.86[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs337539	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs337540	0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs337541	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs337542	0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs337543	0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs337544	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs337545	1.00[CEU][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs337546	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs337547	1.00[CEU][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs337548	0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs337549	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs337550	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs337551	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs337552	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs337553	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs337554	0.83[JPT][hapmap]
rs337556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337557	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs337558	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs337559	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs337560	0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs337561	0.81[ASN][1000 genomes]
rs3808896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs394488	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs405430	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs415902	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743248	0.83[EUR][1000 genomes]
rs4743263	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs4743265	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs507876	0.97[ASN][1000 genomes]
rs526590	0.88[ASN][1000 genomes]
rs529269	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs529278	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs570138	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6478811	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][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	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
7	nsv819653	chr9:101469511-101472192	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv3498543	chr9:101469881-101473129	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv3498544	chr9:101469881-101473129	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs509747	ANKS6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101469000-101470000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
2	chr9:101469000-101470000	Bivalent Enhancer	Spleen	Spleen
3	chr9:101469000-101470600	Flanking Active TSS	HUVEC	blood vessel
4	chr9:101469000-101470800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr9:101469000-101471000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr9:101469000-101471000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:101469000-101471800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
8	chr9:101469200-101470200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:101469200-101470200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:101469200-101470200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:101469200-101470200	Bivalent/Poised TSS	NHLF	lung
12	chr9:101469200-101470400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr9:101469200-101470400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
14	chr9:101469200-101470400	Bivalent Enhancer	Left Ventricle	heart
15	chr9:101469200-101470800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
16	chr9:101469200-101470800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
17	chr9:101469200-101470800	Bivalent/Poised TSS	Brain Substantia Nigra	brain
18	chr9:101469200-101470800	Bivalent Enhancer	Fetal Muscle Leg	muscle
19	chr9:101469200-101470800	Bivalent Enhancer	Placenta	Placenta
20	chr9:101469200-101470800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
21	chr9:101469200-101471000	Bivalent Enhancer	HMEC	breast
22	chr9:101469200-101471800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
23	chr9:101469200-101471800	Enhancers	Liver	Liver
24	chr9:101469200-101472000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
25	chr9:101469200-101472000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
26	chr9:101469200-101472000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
27	chr9:101469200-101472000	Active TSS	Brain Angular Gyrus	brain
28	chr9:101469200-101472200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
29	chr9:101469400-101470000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr9:101469400-101470000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
31	chr9:101469400-101470000	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr9:101469400-101470000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr9:101469400-101470000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
34	chr9:101469400-101470000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
35	chr9:101469400-101470000	Bivalent/Poised TSS	Fetal Brain Female	brain
36	chr9:101469400-101470000	Flanking Active TSS	Psoas Muscle	Psoas
37	chr9:101469400-101470000	Bivalent/Poised TSS	HSMM	muscle
38	chr9:101469400-101470000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
39	chr9:101469400-101470200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:101469400-101470200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr9:101469400-101470200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr9:101469400-101470400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
43	chr9:101469400-101470400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
44	chr9:101469400-101470600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
45	chr9:101469400-101470800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr9:101469400-101470800	Weak transcription	Right Atrium	heart
47	chr9:101469400-101471200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr9:101469400-101472000	Active TSS	Brain Anterior Caudate	brain
49	chr9:101469600-101470000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr9:101469600-101470000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood

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