Variant report

Variant	rs12324121
Chromosome Location	chr15:52608834-52608835
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52584675..52589116-chr15:52605862..52610678,6	MCF-7	breast:
2	chr15:52602148..52604034-chr15:52608756..52610606,2	MCF-7	breast:
3	chr15:52606783..52608986-chr15:52658810..52661433,2	MCF-7	breast:
4	chr15:52606639..52609024-chr15:52615488..52617406,2	K562	blood:

Variant related genes	Relation type
ENSG00000197535	Chromatin interaction
ENSG00000128833	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1001522	0.88[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs10083671	0.88[CEU][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs10083673	0.88[CEU][hapmap];0.91[CHB][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.80[YRI][hapmap]
rs1009157	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];0.86[TSI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10467925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10518687	1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes]
rs12324100	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];0.81[CHB][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes]
rs1464963	0.88[CEU][hapmap];0.91[CHB][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.80[YRI][hapmap]
rs1669858	0.88[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs1669867	0.89[CEU][hapmap];0.91[CHB][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs1724628	0.88[CEU][hapmap];0.81[CHB][hapmap]
rs1724629	0.89[CHB][hapmap]
rs1724631	0.92[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs1724641	0.85[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap]
rs17613475	0.91[MEX][hapmap];0.84[AMR][1000 genomes]
rs2242057	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2242058	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2414150	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2414151	0.89[CEU][hapmap];0.81[CHB][hapmap]
rs2950056	0.87[GIH][hapmap]
rs34926268	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3858907	0.92[CEU][hapmap]
rs4280181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4519295	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4606660	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4776037	0.91[CEU][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4776039	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62015999	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7176061	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs7176482	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7176639	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7181109	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7182150	1.00[CEU][hapmap];0.81[CHB][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs752864	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs752865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs752866	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs8028033	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8033626	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8038386	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs935892	0.88[CEU][hapmap];0.81[CHB][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
rs12324121	MYO5A	cis	cerebellum	SCAN
rs12324121	SHC4	cis	cerebellum	SCAN
rs12324121	MYO5A	cis	parietal	SCAN
rs12324121	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL
rs12324121	SPPL2A	cis	parietal	SCAN
rs12324121	MYO5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52595400-52610800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:52595400-52614200	Weak transcription	Fetal Lung	lung
3	chr15:52595600-52609800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:52595800-52628800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr15:52596000-52611000	Weak transcription	Fetal Stomach	stomach
6	chr15:52596200-52623600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:52597800-52629600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:52597800-52643400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr15:52599200-52611000	Weak transcription	NHLF	lung
10	chr15:52599400-52611000	Weak transcription	Fetal Thymus	thymus
11	chr15:52599400-52611000	Weak transcription	Thymus	Thymus
12	chr15:52599800-52611000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:52599800-52611000	Weak transcription	A549	lung
14	chr15:52600400-52611200	Weak transcription	Colonic Mucosa	Colon
15	chr15:52600600-52611000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr15:52600600-52624200	Weak transcription	Liver	Liver
17	chr15:52600800-52622800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr15:52600800-52646600	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr15:52601000-52610000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr15:52601000-52611000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:52601000-52622600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:52601000-52643400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr15:52601200-52611000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr15:52601200-52615200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:52601200-52622600	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr15:52601400-52609800	Weak transcription	Gastric	stomach
27	chr15:52601400-52611000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:52601400-52611000	Weak transcription	Right Atrium	heart
29	chr15:52601400-52612200	Weak transcription	Right Ventricle	heart
30	chr15:52601600-52622400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr15:52601600-52622800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr15:52601800-52611000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:52601800-52611000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr15:52601800-52616600	Strong transcription	Primary B cells from cord blood	blood
35	chr15:52601800-52621400	Weak transcription	Psoas Muscle	Psoas
36	chr15:52602000-52609400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr15:52602000-52609800	Weak transcription	Pancreas	Pancrea
38	chr15:52602000-52611000	Weak transcription	Esophagus	oesophagus
39	chr15:52602000-52622800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:52602200-52611000	Weak transcription	Fetal Heart	heart
41	chr15:52602200-52622600	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr15:52602600-52622800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr15:52603000-52609000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr15:52603200-52616400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:52603400-52614800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:52603600-52609200	Weak transcription	Ovary	ovary
47	chr15:52603600-52609800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:52603600-52609800	Weak transcription	Aorta	Aorta
49	chr15:52603600-52609800	Weak transcription	Spleen	Spleen
50	chr15:52603600-52611000	Weak transcription	Lung	lung

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