Variant report

Variant	rs11059097
Chromosome Location	chr12:123123684-123123685
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123120054..123123996-chr12:123234682..123237075,4	MCF-7	breast:
2	chr12:123120971..123123822-chr12:123241913..123244089,2	MCF-7	breast:
3	chr12:123118461..123125368-chr12:123234706..123239529,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139726	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1021705	0.85[CEU][hapmap];0.91[JPT][hapmap]
rs10847170	0.96[AFR][1000 genomes]
rs10847329	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10847335	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.85[YRI][hapmap];0.99[ASN][1000 genomes]
rs11058562	0.85[MEX][hapmap]
rs11058710	0.85[CEU][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap]
rs11058797	0.96[AFR][1000 genomes]
rs11059100	0.91[MEX][hapmap]
rs11059237	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs11059257	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11059258	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11611668	0.95[JPT][hapmap];1.00[YRI][hapmap]
rs11614147	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11614277	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817342	0.95[MEX][hapmap]
rs12821949	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2245199	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2936731	0.88[ASN][1000 genomes]
rs34357107	0.92[ASN][1000 genomes]
rs35157148	0.99[ASN][1000 genomes]
rs35297311	0.99[ASN][1000 genomes]
rs59355577	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs612465	0.98[ASN][1000 genomes]
rs61955000	0.84[ASN][1000 genomes]
rs61956121	0.85[AFR][1000 genomes]
rs645348	0.98[ASN][1000 genomes]
rs6489179	0.98[ASN][1000 genomes]
rs7134265	0.97[ASN][1000 genomes]
rs73224116	0.99[ASN][1000 genomes]
rs73224188	0.98[ASN][1000 genomes]
rs7397194	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs7398147	0.98[ASN][1000 genomes]
rs7398861	0.96[AFR][1000 genomes]
rs7398939	0.96[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054458	chr12:123045662-123133545	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11059097	CTSA	trans	parietal	SCAN
rs11059097	RILPL1	cis	parietal	SCAN
rs11059097	KSR2	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123077400-123137600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:123077600-123128200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:123101600-123131000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr12:123105800-123124600	Weak transcription	Fetal Brain Female	brain
5	chr12:123108000-123131400	Weak transcription	NHLF	lung
6	chr12:123108200-123124200	Weak transcription	HMEC	breast
7	chr12:123108400-123128600	Weak transcription	Placenta	Placenta
8	chr12:123109400-123128000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:123110600-123128000	Weak transcription	NHDF-Ad	bronchial
10	chr12:123111600-123136200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:123111800-123127600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:123112000-123126400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:123112000-123128400	Weak transcription	Primary T cells from cord blood	blood
14	chr12:123112200-123128200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:123112200-123130600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr12:123112200-123131200	Weak transcription	Osteobl	bone
17	chr12:123112400-123126600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:123112400-123128200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:123112400-123129400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr12:123112400-123131000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:123114600-123127600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:123115000-123124600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr12:123115000-123128000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:123115000-123131400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:123117600-123127600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:123119000-123127800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr12:123119000-123128000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:123119200-123126800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr12:123119200-123128800	Weak transcription	K562	blood
30	chr12:123119600-123128000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:123119800-123128000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr12:123119800-123128400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr12:123120000-123125400	Weak transcription	Fetal Stomach	stomach
34	chr12:123120000-123128000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr12:123120200-123127600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:123120200-123128000	Weak transcription	HepG2	liver
37	chr12:123120200-123128200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:123120200-123131000	Weak transcription	GM12878-XiMat	blood
39	chr12:123120200-123140800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:123120400-123127800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr12:123120400-123128200	Weak transcription	Fetal Muscle Leg	muscle
42	chr12:123120400-123131000	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr12:123120600-123127600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:123120600-123128000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:123120600-123128200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:123120600-123129400	Weak transcription	Dnd41	blood
47	chr12:123120600-123131200	Weak transcription	A549	lung
48	chr12:123120800-123127000	Weak transcription	Fetal Thymus	thymus
49	chr12:123120800-123128200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:123121800-123127800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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