Variant report

Variant	rs3794565
Chromosome Location	chr15:52655366-52655367
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	chr15:52653880..52655772-chr15:52658306..52660812,2	K562	blood:
2	chr15:52586205..52590641-chr15:52653204..52656400,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128833	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12438578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12440929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12441597	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12900962	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12901814	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1405183	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1405184	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1526169	0.82[MEX][hapmap]
rs1669877	0.82[MEX][hapmap]
rs1724630	0.81[CHB][hapmap]
rs17707852	0.92[YRI][hapmap]
rs1965563	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1972160	0.82[MEX][hapmap]
rs2290332	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2290335	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2290336	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2462847	0.91[MEX][hapmap]
rs28533733	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3794557	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3794564	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3794566	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7176600	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7176830	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8025937	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8030535	0.82[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap]
rs8032995	0.81[AFR][1000 genomes]
rs871488	0.82[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap]
rs940970	0.82[ASW][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3794565	MYO5A	cis	lymphoblastoid	seeQTL
rs3794565	MYO5A	cis	cerebellum	SCAN
rs3794565	KIAA1370	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52607800-52657800	Weak transcription	Small Intestine	intestine
2	chr15:52609800-52677600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:52611800-52675800	Weak transcription	Gastric	stomach
4	chr15:52613600-52666600	Weak transcription	Right Ventricle	heart
5	chr15:52620600-52659200	Weak transcription	Fetal Lung	lung
6	chr15:52621200-52666600	Weak transcription	Fetal Brain Male	brain
7	chr15:52621800-52662200	Weak transcription	Psoas Muscle	Psoas
8	chr15:52630600-52684800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:52631600-52679200	Weak transcription	Fetal Intestine Small	intestine
10	chr15:52632600-52670400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:52632800-52657400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr15:52632800-52662200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr15:52633600-52662200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr15:52638000-52671600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:52640600-52666600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:52641800-52666800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:52643600-52655600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr15:52643800-52655400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:52644000-52664200	Weak transcription	NHLF	lung
20	chr15:52644000-52666600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr15:52644200-52661000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr15:52644200-52680800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr15:52644600-52660200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr15:52644600-52661200	Weak transcription	Thymus	Thymus
25	chr15:52644600-52661600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr15:52644600-52662000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr15:52644600-52662200	Weak transcription	Fetal Muscle Leg	muscle
28	chr15:52644600-52662400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr15:52644600-52662400	Weak transcription	Fetal Stomach	stomach
30	chr15:52644600-52663800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:52644600-52663800	Weak transcription	Spleen	Spleen
32	chr15:52644600-52665400	Weak transcription	A549	lung
33	chr15:52644600-52730200	Weak transcription	Esophagus	oesophagus
34	chr15:52644800-52655600	Weak transcription	Dnd41	blood
35	chr15:52645600-52661200	Weak transcription	NH-A	brain
36	chr15:52645800-52657400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:52645800-52661000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr15:52645800-52661000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:52646000-52660400	Weak transcription	Placenta	Placenta
40	chr15:52646000-52661600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr15:52646200-52657200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr15:52646200-52660600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr15:52646200-52661600	Weak transcription	Left Ventricle	heart
44	chr15:52646200-52663800	Weak transcription	Lung	lung
45	chr15:52646400-52659200	Weak transcription	Colon Smooth Muscle	Colon
46	chr15:52647400-52690600	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr15:52649000-52687200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr15:52649600-52670600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr15:52649600-52677600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr15:52649800-52655400	Strong transcription	Fetal Brain Female	brain

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