Variant report

Variant	rs10861119
Chromosome Location	chr12:104229412-104229413
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104193794..104196589-chr12:104226529..104230835,4	MCF-7	breast:
2	chr12:104227204..104231494-chr12:104232251..104237257,7	MCF-7	breast:
3	chr12:104192744..104195300-chr12:104227670..104230455,2	MCF-7	breast:
4	chr12:104199289..104201376-chr12:104228152..104230435,2	MCF-7	breast:
5	chr12:104229182..104230973-chr12:104526385..104528264,2	K562	blood:
6	chr12:104221267..104222834-chr12:104227996..104230491,2	MCF-7	breast:
7	chr12:104229056..104231950-chr12:104565852..104568001,2	K562	blood:
8	chr12:104198918..104202818-chr12:104225755..104230550,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257327	Chromatin interaction
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10082821	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778288	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861110	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10861111	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10861113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10861114	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10861115	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861116	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10861117	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10861118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111760	1.00[ASN][1000 genomes]
rs11111790	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111794	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111797	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11111802	0.96[AFR][1000 genomes]
rs11111803	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111806	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11111807	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12299784	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12320424	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12368209	1.00[ASN][1000 genomes]
rs12369835	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426059	0.81[ASN][1000 genomes]
rs1370782	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1370783	0.93[EUR][1000 genomes]
rs17034657	0.84[EUR][1000 genomes]
rs3087891	1.00[ASN][1000 genomes]
rs4964197	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4964540	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4964571	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4964574	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4964605	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4964787	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539102	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7138889	1.00[ASN][1000 genomes]
rs7315948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73175816	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10861119	RP11-341G23.4	cis	Whole Blood	GTEx
rs10861119	NT5DC3	cis	Whole Blood	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104218400-104233000	Weak transcription	Gastric	stomach
2	chr12:104218400-104233400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr12:104218800-104232800	Weak transcription	Psoas Muscle	Psoas
4	chr12:104220000-104232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:104222200-104232200	Weak transcription	NHLF	lung
6	chr12:104222600-104232000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:104223200-104233000	Weak transcription	HSMMtube	muscle
8	chr12:104223800-104232000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:104225000-104233600	Weak transcription	Primary T cells from cord blood	blood
10	chr12:104225200-104233200	Weak transcription	Right Atrium	heart
11	chr12:104225600-104233000	Weak transcription	Placenta	Placenta
12	chr12:104226600-104232000	Weak transcription	Stomach Mucosa	stomach
13	chr12:104226800-104232400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr12:104226800-104233200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:104227400-104229800	Flanking Active TSS	K562	blood
16	chr12:104227400-104230000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:104227400-104231200	Enhancers	HepG2	liver
18	chr12:104227600-104232800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:104227800-104231200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:104227800-104233800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr12:104228000-104230400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:104228000-104232200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:104228000-104232400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr12:104228000-104232400	Weak transcription	NHEK	skin
25	chr12:104228000-104232600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:104228000-104232800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:104228000-104232800	Weak transcription	Fetal Stomach	stomach
28	chr12:104228000-104233000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr12:104228000-104233000	Weak transcription	Ovary	ovary
30	chr12:104228000-104233000	Weak transcription	Pancreas	Pancrea
31	chr12:104228200-104233000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr12:104228200-104233400	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr12:104228200-104233800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:104228400-104232400	Weak transcription	NHDF-Ad	bronchial
35	chr12:104228400-104232600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:104228400-104232600	Weak transcription	NH-A	brain
37	chr12:104228400-104233000	Weak transcription	Osteobl	bone
38	chr12:104228400-104233200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr12:104228400-104233200	Weak transcription	Fetal Muscle Leg	muscle
40	chr12:104228600-104229600	Flanking Active TSS	Rectal Smooth Muscle	rectum
41	chr12:104228600-104230200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr12:104228800-104229600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:104228800-104230400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:104228800-104232000	Weak transcription	HMEC	breast
45	chr12:104228800-104232800	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr12:104228800-104233000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr12:104228800-104233200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr12:104229000-104229600	Strong transcription	Aorta	Aorta
49	chr12:104229000-104229800	Weak transcription	Fetal Intestine Large	intestine
50	chr12:104229000-104231200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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