Variant report

Variant	rs1058142
Chromosome Location	chr13:52342206-52342207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52306205..52308495-chr13:52341263..52344229,2	MCF-7	breast:
2	chr13:52337340..52339624-chr13:52341106..52343794,2	K562	blood:
3	chr13:52156494..52159056-chr13:52340175..52342392,2	MCF-7	breast:
4	chr13:52337387..52338953-chr13:52340888..52343879,2	MCF-7	breast:
5	chr13:52024690..52027265-chr13:52341888..52344446,2	K562	blood:

Variant related genes	Relation type
ENSG00000102786	Chromatin interaction
ENSG00000139668	Chromatin interaction
ENSG00000236778	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1058141	0.93[ASW][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs1060562	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10676	0.82[LWK][hapmap];0.90[MKK][hapmap];0.95[YRI][hapmap]
rs12146894	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12427805	0.93[ASW][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs12430600	0.93[ASW][hapmap];0.96[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs17069413	0.93[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs17075849	0.84[YRI][hapmap]
rs2011276	0.89[AFR][1000 genomes]
rs2296027	0.93[LWK][hapmap];0.86[MKK][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs2408491	0.93[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs2897944	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55910561	0.91[AFR][1000 genomes]
rs57837262	0.89[AFR][1000 genomes]
rs73199750	0.88[AFR][1000 genomes]
rs7321346	0.81[AFR][1000 genomes]
rs7329391	0.86[ASW][hapmap];0.93[LWK][hapmap];0.82[MKK][hapmap]
rs9526795	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535714	0.80[JPT][hapmap]
rs9535748	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9535754	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568662	1.00[YRI][hapmap]
rs9596572	0.89[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription 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	38 gene(s)	inside rSNPs	diseases
3	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv455887	chr13:52318522-52405251	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv561645	chr13:52318522-52405251	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1058142	WDFY2	cis	parietal	SCAN
rs1058142	TRIM13	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52308200-52342800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr13:52323000-52343400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr13:52324800-52342600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr13:52326000-52342600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr13:52327600-52343200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr13:52327800-52343000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr13:52330600-52355600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr13:52332600-52342800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr13:52333000-52342600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr13:52333000-52343600	Weak transcription	Psoas Muscle	Psoas
11	chr13:52333200-52342400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr13:52334400-52343800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr13:52335000-52343200	Weak transcription	Ovary	ovary
14	chr13:52335200-52347000	Weak transcription	Fetal Brain Male	brain
15	chr13:52335200-52348000	Weak transcription	Fetal Brain Female	brain
16	chr13:52336400-52342400	Weak transcription	Fetal Heart	heart
17	chr13:52336600-52342400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr13:52336800-52342400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr13:52338600-52342600	Strong transcription	NHEK	skin
20	chr13:52338800-52342400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr13:52338800-52343000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr13:52339200-52342600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr13:52339400-52342400	Weak transcription	Left Ventricle	heart
24	chr13:52339400-52342400	Weak transcription	Right Atrium	heart
25	chr13:52339400-52342400	Weak transcription	Right Ventricle	heart
26	chr13:52339400-52342400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr13:52339400-52342800	Strong transcription	Primary B cells from cord blood	blood
28	chr13:52339400-52343400	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr13:52339400-52343800	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr13:52339400-52343800	Weak transcription	Brain Anterior Caudate	brain
31	chr13:52339400-52343800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr13:52339400-52345000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr13:52339400-52347000	Weak transcription	A549	lung
34	chr13:52339400-52347600	Weak transcription	Aorta	Aorta
35	chr13:52339400-52347600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr13:52339400-52347800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr13:52339400-52349600	Weak transcription	Placenta	Placenta
38	chr13:52339400-52352000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr13:52339400-52356200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr13:52339400-52357400	Weak transcription	Colonic Mucosa	Colon
41	chr13:52339600-52342400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr13:52339600-52342800	Weak transcription	NHDF-Ad	bronchial
43	chr13:52339600-52343400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr13:52339600-52343600	Weak transcription	Stomach Mucosa	stomach
45	chr13:52339600-52344000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr13:52339600-52344400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr13:52339600-52356800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr13:52339600-52361400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr13:52339600-52375000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr13:52339800-52342400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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