Variant report

Variant	rs35958407
Chromosome Location	chr15:72979501-72979502
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr15:72979424-72979699	HepG2	liver:	n/a	n/a
2	CTCF	chr15:72979491-72979531	LNCaP	prostate:	n/a	n/a
3	ZNF384	chr15:72978277-72979633	K562	blood:	n/a	n/a
4	YY1	chr15:72979429-72979655	K562	blood:	n/a	n/a
5	CTCF	chr15:72979477-72979581	MCF-7	breast:	n/a	n/a
6	HCFC1	chr15:72977649-72979595	Hela-S3	cervix:	n/a	n/a
7	ZNF384	chr15:72978549-72979539	GM12878	blood:	n/a	n/a
8	YY1	chr15:72979414-72979638	K562	blood:	n/a	n/a
9	HA-E2F1	chr15:72977908-72979833	MCF-7	breast:	n/a	chr15:72978241-72978253
10	POLR2A	chr15:72979332-72980565	K562	blood:	n/a	n/a
11	MXI1	chr15:72977328-72979684	SK-N-SH	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:72978938..72981317-chr15:73074560..73077463,3	K562	blood:
2	chr15:72971779..72975423-chr15:72976170..72980827,7	K562	blood:
3	chr15:72521683..72524680-chr15:72976957..72979803,2	K562	blood:
4	chr15:72973101..72975344-chr15:72976692..72980792,4	MCF-7	breast:
5	chr15:72562851..72564645-chr15:72977653..72979663,2	K562	blood:
6	chr15:72978938..72981317-chr15:73074560..73077463,2	K562	blood:
7	chr15:72978470..72980550-chr15:73014196..73015991,2	K562	blood:
8	chr15:72764850..72767674-chr15:72977020..72979928,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000261281	TF binding region
HIGD2B	TF binding region
ENSG00000166233	Chromatin interaction
ENSG00000159322	Chromatin interaction
ENSG00000140463	Chromatin interaction
ENSG00000137817	Chromatin interaction
ENSG00000260898	Chromatin interaction
ENSG00000261281	Chromatin interaction
ENSG00000261423	Chromatin interaction
ENSG00000067225	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11072384	0.89[ASN][1000 genomes]
rs12440951	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12441084	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12592955	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12594667	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12594844	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16957293	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2278543	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28502551	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3179616	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34337823	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35136341	0.97[EUR][1000 genomes]
rs3759870	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3850988	0.90[ASN][1000 genomes]
rs4776611	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4777528	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4777529	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4777530	0.97[EUR][1000 genomes]
rs4777531	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4777537	0.94[EUR][1000 genomes]
rs4777538	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57621041	0.97[EUR][1000 genomes]
rs58600393	0.95[EUR][1000 genomes]
rs59049627	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59152128	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60405894	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60601886	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60674997	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61311866	0.91[EUR][1000 genomes]
rs62017593	0.97[EUR][1000 genomes]
rs62017598	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72662112	0.96[EUR][1000 genomes]
rs72737337	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8033644	0.81[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	esv2758386	chr15:72819785-73120560	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv2760039	chr15:72819785-73120560	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv428307	chr15:72819785-73120560	Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	esv3430383	chr15:72821093-73035167	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35958407	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72977400-72979600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:72977400-72979600	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr15:72977400-72979800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:72977400-72980000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:72977400-72980200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr15:72977600-72979600	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr15:72977600-72979600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:72977600-72979800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:72977600-72979800	Active TSS	Fetal Intestine Large	intestine
10	chr15:72977600-72979800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr15:72977600-72979800	Active TSS	Thymus	Thymus
12	chr15:72977800-72979600	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr15:72977800-72979600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:72977800-72979600	Active TSS	Fetal Kidney	kidney
15	chr15:72977800-72979600	Active TSS	Psoas Muscle	Psoas
16	chr15:72977800-72979600	Active TSS	Sigmoid Colon	Sigmoid Colon
17	chr15:72977800-72979600	Active TSS	HMEC	breast
18	chr15:72977800-72979800	Active TSS	Fetal Intestine Small	intestine
19	chr15:72977800-72980000	Active TSS	Colonic Mucosa	Colon
20	chr15:72978000-72979600	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr15:72978000-72979600	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr15:72978000-72979600	Active TSS	Primary T cells from cord blood	blood
23	chr15:72978000-72979600	Active TSS	Brain Germinal Matrix	brain
24	chr15:72978000-72979600	Active TSS	Colon Smooth Muscle	Colon
25	chr15:72978000-72979600	Active TSS	Fetal Stomach	stomach
26	chr15:72978000-72979600	Active TSS	Ovary	ovary
27	chr15:72978000-72979600	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr15:72978000-72979600	Active TSS	NHEK	skin
29	chr15:72978000-72979800	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr15:72978000-72979800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:72978000-72979800	Active TSS	HSMMtube	muscle
32	chr15:72978000-72980000	Active TSS	K562	blood
33	chr15:72978000-72980200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:72978200-72979600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:72978200-72979600	Active TSS	Liver	Liver
36	chr15:72978200-72979600	Active TSS	Brain Hippocampus Middle	brain
37	chr15:72978200-72979600	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr15:72978200-72979600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr15:72978200-72979600	Active TSS	Placenta	Placenta
40	chr15:72978200-72979600	Active TSS	Rectal Smooth Muscle	rectum
41	chr15:72978200-72979600	Active TSS	NH-A	brain
42	chr15:72978200-72979600	Active TSS	NHDF-Ad	bronchial
43	chr15:72978200-72979600	Active TSS	NHLF	lung
44	chr15:72978200-72979800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:72978200-72979800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:72978200-72979800	Active TSS	Muscle Satellite Cultured Cells	--
47	chr15:72978200-72979800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:72978200-72979800	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr15:72978200-72979800	Active TSS	Stomach Smooth Muscle	stomach
50	chr15:72978200-72979800	Active TSS	Hela-S3	cervix

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