Variant report

Variant	rs60060012
Chromosome Location	chr1:150558997-150558998
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:150550651..150553776-chr1:150557579..150562132,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143384	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1053701	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204665	0.86[ASN][1000 genomes]
rs11204674	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11585460	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12034302	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036914	0.88[ASN][1000 genomes]
rs12042580	0.93[ASN][1000 genomes]
rs12045807	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28744536	0.86[ASN][1000 genomes]
rs61820166	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61820168	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61820170	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587515	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6672667	0.88[ASN][1000 genomes]
rs7517	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7543465	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv535155	chr1:150535349-150582395	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
3	nsv535156	chr1:150540117-150575941	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	nsv535157	chr1:150552692-150575941	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60060012	CTSK	cis	Artery Aorta	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150553000-150559200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:150553000-150560600	Weak transcription	Right Atrium	heart
3	chr1:150553000-150562600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:150553000-150572800	Weak transcription	Thymus	Thymus
5	chr1:150553000-150583200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:150553200-150564200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:150553200-150566000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:150553200-150568400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:150553200-150569400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:150553200-150569400	Weak transcription	Fetal Thymus	thymus
11	chr1:150553200-150572600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:150553200-150572600	Weak transcription	Fetal Brain Female	brain
13	chr1:150553200-150572800	Weak transcription	Brain Angular Gyrus	brain
14	chr1:150553200-150577600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:150553200-150581800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:150553200-150581800	Weak transcription	Dnd41	blood
17	chr1:150553200-150583200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:150553200-150592000	Weak transcription	Fetal Kidney	kidney
19	chr1:150553800-150568000	Weak transcription	HSMM	muscle
20	chr1:150553800-150572600	Weak transcription	Lung	lung
21	chr1:150553800-150576800	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:150554000-150560400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:150554000-150568400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:150554000-150568600	Weak transcription	Hela-S3	cervix
25	chr1:150554000-150572000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:150554000-150583200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:150554200-150568400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:150554400-150572600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr1:150555400-150568400	Weak transcription	Osteobl	bone
30	chr1:150555400-150572600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr1:150555400-150582600	Weak transcription	Primary B cells from cord blood	blood
32	chr1:150555600-150568400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:150555600-150568400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:150556000-150564800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:150557200-150568400	Weak transcription	Fetal Intestine Small	intestine
36	chr1:150557400-150564000	Weak transcription	Fetal Stomach	stomach
37	chr1:150558800-150568400	Weak transcription	Duodenum Mucosa	Duodenum

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