Variant report

Variant	rs16956623
Chromosome Location	chr15:72536695-72536696
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:72532567..72537112-chr15:72562138..72566165,7	MCF-7	breast:
2	chr15:72498523..72500643-chr15:72535160..72537562,2	K562	blood:

Variant related genes	Relation type
ENSG00000137817	Chromatin interaction
ENSG00000067225	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1000281	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1035744	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10851850	0.94[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072349	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11072350	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11630170	0.84[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs11630611	0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs11633327	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11634622	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11637611	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12442886	0.84[CEU][hapmap]
rs12904652	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13858	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs2052713	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2278987	0.83[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs2415134	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35603965	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3759900	0.80[AMR][1000 genomes]
rs3759902	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4506844	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55763892	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62022788	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62022789	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6494992	0.83[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6494997	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs713048	0.84[CEU][hapmap]
rs7162299	0.89[JPT][hapmap]
rs7169264	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7170456	0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7175197	0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7175792	0.84[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes]
rs7179427	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7179942	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7183196	0.84[CEU][hapmap]
rs7183810	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8023788	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8025939	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8027164	0.84[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs8027647	0.91[EUR][1000 genomes]
rs8028115	0.84[CEU][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap]
rs8030815	0.84[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs8031386	0.80[AMR][1000 genomes]
rs8032222	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8038007	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8040828	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8192362	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[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	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
3	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16956623	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72524800-72551400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:72525400-72548600	Weak transcription	Fetal Heart	heart
3	chr15:72530400-72542200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:72530400-72563400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:72530600-72542000	Weak transcription	Stomach Mucosa	stomach
6	chr15:72530600-72545600	Weak transcription	Small Intestine	intestine
7	chr15:72530800-72561200	Strong transcription	Adipose Nuclei	Adipose
8	chr15:72531000-72537000	Strong transcription	Skeletal Muscle Female	skeletal muscle
9	chr15:72531000-72539000	Strong transcription	Placenta	Placenta
10	chr15:72531000-72562400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:72531000-72563000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:72531000-72563000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:72531000-72563400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:72531200-72539000	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr15:72531200-72562800	Strong transcription	Fetal Muscle Leg	muscle
16	chr15:72531400-72537000	Strong transcription	HSMMtube	muscle
17	chr15:72531400-72538600	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:72531400-72538800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:72531400-72542000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr15:72531600-72539800	Strong transcription	Fetal Brain Female	brain
21	chr15:72531800-72561400	Strong transcription	Stomach Smooth Muscle	stomach
22	chr15:72532000-72537000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr15:72532000-72537000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:72532000-72537200	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr15:72532000-72537400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:72532000-72537400	Strong transcription	Brain Angular Gyrus	brain
27	chr15:72532000-72537400	Strong transcription	Psoas Muscle	Psoas
28	chr15:72532000-72539800	Strong transcription	Primary T cells from cord blood	blood
29	chr15:72532000-72543200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr15:72532000-72562600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:72532200-72537000	Strong transcription	Osteobl	bone
32	chr15:72532200-72537200	Strong transcription	Fetal Lung	lung
33	chr15:72532200-72537200	Strong transcription	NH-A	brain
34	chr15:72532200-72538000	Strong transcription	Primary B cells from cord blood	blood
35	chr15:72532200-72538200	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr15:72532200-72538200	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr15:72532200-72538400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:72532200-72538400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr15:72532200-72538400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr15:72532200-72538800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr15:72532200-72561000	Strong transcription	Liver	Liver
42	chr15:72532200-72561000	Strong transcription	Fetal Intestine Large	intestine
43	chr15:72532200-72561600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr15:72532200-72562200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:72532200-72563000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:72532400-72537000	Strong transcription	NHEK	skin
47	chr15:72532400-72538400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr15:72532400-72538400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:72532400-72539000	Strong transcription	A549	lung
50	chr15:72532400-72540400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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