Variant report

Variant	rs4743278
Chromosome Location	chr9:101558024-101558025
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100683358..100685652-chr9:101557664..101560368,2	K562	blood:
2	chr9:101555483..101562112-chr9:101568669..101573087,9	K562	blood:
3	chr9:101534630..101537208-chr9:101556445..101558370,2	MCF-7	breast:
4	chr9:101557242..101560519-chr9:101566443..101572716,8	MCF-7	breast:
5	chr9:101546085..101548581-chr9:101557389..101560839,3	MCF-7	breast:
6	chr9:101556573..101560424-chr9:101566029..101574080,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165138	Chromatin interaction
ENSG00000136932	Chromatin interaction
ENSG00000119514	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10121153	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1022796	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739690	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10760475	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10760479	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10760494	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10819266	0.85[ASN][1000 genomes]
rs10819308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10819320	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10987747	0.81[EUR][1000 genomes]
rs10987749	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10987771	0.80[EUR][1000 genomes]
rs11791440	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12056975	0.87[EUR][1000 genomes]
rs1543506	0.80[EUR][1000 genomes]
rs1555519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146255	0.80[EUR][1000 genomes]
rs33998698	0.80[EUR][1000 genomes]
rs3933477	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742737	0.92[ASN][1000 genomes]
rs4742738	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4742741	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4742745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743282	0.90[ASN][1000 genomes]
rs6478839	0.89[ASN][1000 genomes]
rs6478845	0.89[ASN][1000 genomes]
rs7018907	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7027405	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7027771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038640	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7047722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7357783	0.90[ASN][1000 genomes]
rs7469116	0.93[ASN][1000 genomes]
rs7853904	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7861186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7865233	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9886821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv3376962	chr9:101557781-101559879	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4743278	ANKS6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101556800-101559400	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr9:101557200-101558200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr9:101557200-101558200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr9:101557200-101558200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr9:101557200-101558200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
6	chr9:101557200-101558200	Flanking Active TSS	Hela-S3	cervix
7	chr9:101557200-101558200	Flanking Active TSS	NHDF-Ad	bronchial
8	chr9:101557200-101558400	Enhancers	Spleen	Spleen
9	chr9:101557200-101559000	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr9:101557200-101559400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:101557400-101558200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr9:101557400-101558200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr9:101557400-101558200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr9:101557400-101558200	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr9:101557400-101558200	Flanking Active TSS	Brain Angular Gyrus	brain
16	chr9:101557400-101558200	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr9:101557400-101558200	Flanking Active TSS	Fetal Intestine Large	intestine
18	chr9:101557400-101558200	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr9:101557400-101558200	Flanking Active TSS	NHEK	skin
20	chr9:101557400-101558200	Flanking Active TSS	NHLF	lung
21	chr9:101557400-101558200	Flanking Active TSS	Osteobl	bone
22	chr9:101557400-101558400	Enhancers	Fetal Heart	heart
23	chr9:101557400-101559000	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr9:101557400-101559200	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr9:101557400-101559400	Active TSS	H9 Cell Line	embryonic stem cell
26	chr9:101557600-101558200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr9:101557600-101558200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:101557600-101558200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr9:101557600-101558200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:101557600-101558200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:101557600-101558200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr9:101557600-101558200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr9:101557600-101558200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr9:101557600-101558200	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr9:101557600-101558200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr9:101557600-101558200	Flanking Active TSS	Colon Smooth Muscle	Colon
37	chr9:101557600-101558200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr9:101557600-101558200	Flanking Active TSS	Fetal Muscle Trunk	muscle
39	chr9:101557600-101558200	Flanking Active TSS	Fetal Muscle Leg	muscle
40	chr9:101557600-101558200	Flanking Active TSS	Lung	lung
41	chr9:101557600-101558200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr9:101557600-101558200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
43	chr9:101557600-101558200	Flanking Active TSS	Rectal Smooth Muscle	rectum
44	chr9:101557600-101558200	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr9:101557600-101558200	Flanking Active TSS	Dnd41	blood
46	chr9:101557600-101558200	Flanking Active TSS	HepG2	liver
47	chr9:101557600-101558200	Flanking Active TSS	HMEC	breast
48	chr9:101557600-101558200	Flanking Active TSS	K562	blood
49	chr9:101557600-101558400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr9:101557600-101558400	Flanking Active TSS	Fetal Brain Female	brain

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