Variant report

Variant	rs34197242
Chromosome Location	chr15:52838988-52838989
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52834312..52836237-chr15:52837980..52840201,2	MCF-7	breast:
2	chr15:52838384..52840575-chr15:52859458..52861427,2	MCF-7	breast:
3	chr15:52838405..52842641-chr15:52848798..52852133,5	MCF-7	breast:
4	chr15:52836622..52839186-chr15:52841792..52845841,4	K562	blood:
5	chr15:52833192..52836682-chr15:52837514..52841667,6	K562	blood:
6	chr15:52837831..52839348-chr15:52842783..52844541,2	MCF-7	breast:
7	chr15:52837261..52840412-chr15:52840986..52844425,3	K562	blood:

Variant related genes	Relation type
ENSG00000128989	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12232368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12592429	1.00[MEX][hapmap]
rs12899847	0.88[MEX][hapmap]
rs12915892	1.00[ASW][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap]
rs1568954	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1724593	0.82[MEX][hapmap]
rs2414159	0.88[AMR][1000 genomes]
rs35014728	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57187323	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6493566	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7181784	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1047775	chr15:52822050-52912228	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34197242	MYO5A	cis	cerebellum	SCAN
rs34197242	SECISBP2L	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52822200-52839600	Weak transcription	Right Atrium	heart
2	chr15:52828800-52850400	Weak transcription	Fetal Brain Male	brain
3	chr15:52830000-52841200	Weak transcription	HepG2	liver
4	chr15:52835800-52845800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:52836200-52851400	Weak transcription	Fetal Kidney	kidney
6	chr15:52836400-52842200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr15:52836400-52855200	Weak transcription	Small Intestine	intestine
8	chr15:52836600-52844000	Weak transcription	K562	blood
9	chr15:52836600-52844200	Weak transcription	Psoas Muscle	Psoas
10	chr15:52836600-52846000	Weak transcription	Stomach Mucosa	stomach
11	chr15:52836600-52849000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:52836800-52848200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr15:52837200-52844800	Strong transcription	A549	lung
14	chr15:52837400-52844000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr15:52837400-52844600	Strong transcription	HSMM	muscle
16	chr15:52837400-52847000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:52837400-52849400	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr15:52837600-52839000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:52837600-52839000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr15:52837600-52839200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:52837600-52839200	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr15:52837600-52839200	Strong transcription	Fetal Brain Female	brain
23	chr15:52837600-52849400	Strong transcription	NHDF-Ad	bronchial
24	chr15:52837600-52852000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr15:52837800-52839000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
26	chr15:52837800-52839000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
27	chr15:52837800-52839000	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr15:52837800-52840000	Strong transcription	Fetal Heart	heart
29	chr15:52837800-52840600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:52837800-52841000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
31	chr15:52837800-52842400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr15:52837800-52846000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:52837800-52853000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr15:52838000-52839000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:52838000-52839000	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr15:52838000-52839000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
37	chr15:52838000-52839000	Strong transcription	Brain Hippocampus Middle	brain
38	chr15:52838000-52839000	ZNF genes & repeats	Spleen	Spleen
39	chr15:52838000-52839200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:52838000-52839200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:52838000-52839200	ZNF genes & repeats	GM12878-XiMat	blood
42	chr15:52838000-52839200	Strong transcription	NHLF	lung
43	chr15:52838000-52839400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr15:52838000-52839600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr15:52838000-52839800	Strong transcription	HMEC	breast
46	chr15:52838000-52840400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:52838000-52843400	Strong transcription	Liver	Liver
48	chr15:52838000-52844000	Strong transcription	Adipose Nuclei	Adipose
49	chr15:52838000-52844600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:52838000-52845200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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