Variant report

Variant	rs3933477
Chromosome Location	chr9:101552096-101552097
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:101483008..101485342-chr9:101550815..101552650,2	K562	blood:
2	chr9:101545059..101549166-chr9:101549298..101553118,4	MCF-7	breast:
3	chr9:101545621..101549470-chr9:101551390..101554188,5	MCF-7	breast:
4	chr9:101539424..101541523-chr9:101551442..101554198,3	MCF-7	breast:
5	chr9:101550931..101552651-chr9:101871439..101873531,2	K562	blood:
6	chr9:101550225..101553756-chr9:101569289..101571539,3	MCF-7	breast:
7	chr9:101551293..101553847-chr9:101568036..101571328,4	K562	blood:
8	chr9:101550194..101555244-chr9:101566657..101571786,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000165138	Chromatin interaction
ENSG00000119514	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10121153	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1022796	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10739690	0.87[ASN][1000 genomes]
rs10760475	0.84[ASN][1000 genomes]
rs10760479	0.85[ASN][1000 genomes]
rs10760494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819266	0.81[ASN][1000 genomes]
rs10819308	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10819320	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10987747	0.83[EUR][1000 genomes]
rs10987749	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10987771	0.84[EUR][1000 genomes]
rs11791440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12056975	0.91[EUR][1000 genomes]
rs1543506	0.84[EUR][1000 genomes]
rs1555519	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2146255	0.84[EUR][1000 genomes]
rs33998698	0.84[EUR][1000 genomes]
rs4742737	0.86[ASN][1000 genomes]
rs4742738	0.85[ASN][1000 genomes]
rs4742741	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4742745	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743278	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4743281	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4743282	0.85[ASN][1000 genomes]
rs6478839	0.84[ASN][1000 genomes]
rs6478845	0.83[ASN][1000 genomes]
rs7018907	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7020056	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7027405	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7027771	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7038640	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047722	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7357783	0.85[ASN][1000 genomes]
rs7469116	0.88[ASN][1000 genomes]
rs7853904	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7861186	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7865233	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9886821	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3933477	ANKS6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101494400-101553000	Weak transcription	Fetal Heart	heart
2	chr9:101506800-101553400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr9:101508600-101557400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr9:101514400-101553400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr9:101518800-101557200	Weak transcription	Psoas Muscle	Psoas
6	chr9:101521200-101557600	Weak transcription	Fetal Brain Male	brain
7	chr9:101530400-101557800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:101533800-101553200	Strong transcription	Fetal Stomach	stomach
9	chr9:101534000-101557600	Weak transcription	Right Atrium	heart
10	chr9:101535600-101553400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr9:101535800-101553400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr9:101535800-101557400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr9:101536000-101553200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:101536000-101557600	Weak transcription	Primary B cells from cord blood	blood
15	chr9:101536200-101553400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr9:101536600-101557600	Weak transcription	Brain Germinal Matrix	brain
17	chr9:101537000-101557400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:101538200-101553000	Weak transcription	NH-A	brain
19	chr9:101538800-101552400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:101539000-101553000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:101541600-101553000	Weak transcription	Brain Anterior Caudate	brain
22	chr9:101542000-101553200	Weak transcription	HUVEC	blood vessel
23	chr9:101542600-101553200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:101544200-101552200	Weak transcription	Spleen	Spleen
25	chr9:101544200-101557600	Weak transcription	Colonic Mucosa	Colon
26	chr9:101544800-101557600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr9:101545200-101553000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr9:101545200-101557200	Weak transcription	Liver	Liver
29	chr9:101545400-101553200	Weak transcription	Brain Substantia Nigra	brain
30	chr9:101545800-101553000	Weak transcription	Hela-S3	cervix
31	chr9:101546200-101553000	Weak transcription	Osteobl	bone
32	chr9:101546200-101557600	Weak transcription	Left Ventricle	heart
33	chr9:101546400-101557200	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr9:101546600-101552200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:101546600-101552200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr9:101546600-101552200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr9:101546600-101553200	Weak transcription	Placenta	Placenta
38	chr9:101546800-101553000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr9:101547000-101553400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr9:101547000-101557000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr9:101547400-101553600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr9:101547800-101553200	Strong transcription	Primary T cells from cord blood	blood
43	chr9:101548200-101552800	Weak transcription	NHDF-Ad	bronchial
44	chr9:101548200-101553000	Weak transcription	Adipose Nuclei	Adipose
45	chr9:101549000-101552600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:101549000-101553200	Strong transcription	K562	blood
47	chr9:101549200-101552400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr9:101549200-101552400	Strong transcription	Brain Cingulate Gyrus	brain
49	chr9:101549400-101552400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr9:101549600-101552400	Strong transcription	Fetal Muscle Trunk	muscle

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