Variant report

Variant	rs12324100
Chromosome Location	chr15:52641688-52641689
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52640299..52642947-chr15:52856133..52857726,2	MCF-7	breast:
2	chr15:52633711..52635722-chr15:52639445..52641864,2	MCF-7	breast:
3	chr15:52626828..52629025-chr15:52639618..52642359,2	MCF-7	breast:
4	chr15:52547210..52549304-chr15:52640088..52643022,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128833	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1001522	0.88[CEU][hapmap]
rs10083671	0.88[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap]
rs10083673	0.88[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs1009157	0.83[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[LWK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10467925	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10518687	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12324121	1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12914979	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1464963	0.88[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs1669858	0.88[CEU][hapmap]
rs1669867	0.89[CEU][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs1724628	0.88[CEU][hapmap]
rs1724631	0.95[GIH][hapmap];0.87[TSI][hapmap]
rs1724641	0.85[CEU][hapmap]
rs17613475	0.96[MEX][hapmap]
rs2242057	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2242058	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2414150	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2414151	0.89[CEU][hapmap]
rs2950056	0.89[GIH][hapmap]
rs3858907	0.92[CEU][hapmap]
rs4280181	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4519295	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4606660	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4776037	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4776039	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62015999	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7176482	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7176639	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7182150	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs752864	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs752865	1.00[CEU][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs752866	1.00[CEU][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs8028033	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8033626	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8038386	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs935892	0.88[CEU][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12324100	MYO5A	Cis_1M	lymphoblastoid	RTeQTL
rs12324100	SHC4	cis	cerebellum	SCAN
rs12324100	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL
rs12324100	SPPL2A	cis	parietal	SCAN
rs12324100	MYO5A	cis	cerebellum	SCAN
rs12324100	MYO5A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52597800-52643400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:52600800-52646600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr15:52601000-52643400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr15:52607800-52657800	Weak transcription	Small Intestine	intestine
5	chr15:52609800-52677600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:52610000-52643400	Weak transcription	Placenta	Placenta
7	chr15:52611600-52650200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:52611800-52675800	Weak transcription	Gastric	stomach
9	chr15:52613000-52642600	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:52613600-52666600	Weak transcription	Right Ventricle	heart
11	chr15:52614800-52642600	Weak transcription	Esophagus	oesophagus
12	chr15:52614800-52653200	Weak transcription	Colonic Mucosa	Colon
13	chr15:52620000-52652200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:52620600-52659200	Weak transcription	Fetal Lung	lung
15	chr15:52621200-52666600	Weak transcription	Fetal Brain Male	brain
16	chr15:52621800-52662200	Weak transcription	Psoas Muscle	Psoas
17	chr15:52623800-52644200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr15:52624600-52642400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr15:52627000-52646600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:52630600-52684800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr15:52631600-52679200	Weak transcription	Fetal Intestine Small	intestine
22	chr15:52632600-52643200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr15:52632600-52643400	Weak transcription	Lung	lung
24	chr15:52632600-52644200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:52632600-52670400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr15:52632800-52642600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr15:52632800-52642600	Weak transcription	NHEK	skin
28	chr15:52632800-52657400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr15:52632800-52662200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr15:52633000-52643800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr15:52633600-52645400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr15:52633600-52662200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr15:52633800-52642800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr15:52633800-52643200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:52635200-52648200	Strong transcription	Primary B cells from peripheral blood	blood
36	chr15:52636000-52643400	Weak transcription	Right Atrium	heart
37	chr15:52636400-52642600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr15:52636800-52642600	Weak transcription	NH-A	brain
39	chr15:52637000-52642600	Weak transcription	A549	lung
40	chr15:52638000-52671600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr15:52638200-52645800	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr15:52638800-52642600	Weak transcription	Brain Substantia Nigra	brain
43	chr15:52639400-52644600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:52640000-52641800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:52640000-52641800	Enhancers	Fetal Heart	heart
46	chr15:52640200-52641800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:52640200-52641800	Strong transcription	Aorta	Aorta
48	chr15:52640200-52642600	Enhancers	HSMMtube	muscle
49	chr15:52640200-52644600	Strong transcription	GM12878-XiMat	blood
50	chr15:52640200-52646200	Strong transcription	Brain Cingulate Gyrus	brain

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