Variant report

Variant	rs1058141
Chromosome Location	chr13:52342546-52342547
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	chr13:52337387..52338953-chr13:52340888..52343879,2	MCF-7	breast:
4	chr13:52024690..52027265-chr13:52341888..52344446,2	K562	blood:

Variant related genes	Relation type
ENSG00000102786	Chromatin interaction
ENSG00000236778	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1058142	0.93[ASW][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs1060562	0.88[AFR][1000 genomes]
rs10676	0.92[GIH][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12146894	0.86[ASW][hapmap];0.85[MKK][hapmap]
rs12427805	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12428478	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12430600	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12430760	0.85[CEU][hapmap];0.88[AMR][1000 genomes]
rs17069413	1.00[ASW][hapmap];0.85[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs17075849	0.82[CEU][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs17531181	0.96[GIH][hapmap];1.00[MEX][hapmap]
rs2011276	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2296027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408491	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2897944	0.81[ASW][hapmap]
rs4399447	0.81[AMR][1000 genomes]
rs55910561	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57280031	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57837262	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59291282	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73199739	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73199742	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73199750	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7321346	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs7329391	0.93[ASW][hapmap];0.96[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[AMR][1000 genomes]
rs74086223	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs7985214	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8001480	0.85[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes]
rs9526795	0.93[ASW][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs9535754	0.86[ASW][hapmap];0.93[LWK][hapmap];0.80[MKK][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes]
rs9568662	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs9596572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9596573	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No data

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	chr13:52334400-52343800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr13:52335000-52343200	Weak transcription	Ovary	ovary
13	chr13:52335200-52347000	Weak transcription	Fetal Brain Male	brain
14	chr13:52335200-52348000	Weak transcription	Fetal Brain Female	brain
15	chr13:52338600-52342600	Strong transcription	NHEK	skin
16	chr13:52338800-52343000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr13:52339200-52342600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr13:52339400-52342800	Strong transcription	Primary B cells from cord blood	blood
19	chr13:52339400-52343400	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr13:52339400-52343800	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr13:52339400-52343800	Weak transcription	Brain Anterior Caudate	brain
22	chr13:52339400-52343800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr13:52339400-52345000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr13:52339400-52347000	Weak transcription	A549	lung
25	chr13:52339400-52347600	Weak transcription	Aorta	Aorta
26	chr13:52339400-52347600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr13:52339400-52347800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr13:52339400-52349600	Weak transcription	Placenta	Placenta
29	chr13:52339400-52352000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr13:52339400-52356200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr13:52339400-52357400	Weak transcription	Colonic Mucosa	Colon
32	chr13:52339600-52342800	Weak transcription	NHDF-Ad	bronchial
33	chr13:52339600-52343400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr13:52339600-52343600	Weak transcription	Stomach Mucosa	stomach
35	chr13:52339600-52344000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr13:52339600-52344400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr13:52339600-52356800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr13:52339600-52361400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr13:52339600-52375000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr13:52339800-52343000	Strong transcription	HSMM	muscle
41	chr13:52339800-52343400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr13:52339800-52343400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr13:52339800-52343400	Weak transcription	Brain Substantia Nigra	brain
44	chr13:52339800-52343600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr13:52339800-52345600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr13:52339800-52345600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr13:52339800-52346200	Strong transcription	Primary T cells from cord blood	blood
48	chr13:52339800-52359800	Weak transcription	Colon Smooth Muscle	Colon
49	chr13:52339800-52371400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr13:52339800-52375200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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