Variant report

Variant	rs4964623
Chromosome Location	chr12:104222742-104222743
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104221407..104223311-chr12:104252551..104254594,2	MCF-7	breast:
2	chr12:104206123..104208804-chr12:104221926..104227695,4	K562	blood:
3	chr12:104221570..104225596-chr12:104232317..104237466,6	MCF-7	breast:
4	chr12:104221267..104222834-chr12:104227996..104230491,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111696	Chromatin interaction
ENSG00000257327	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10861104	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10861105	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10861109	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111778	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11111786	0.81[EUR][1000 genomes]
rs11111788	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11111789	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11111791	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11111792	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11111793	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11111795	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11111796	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11111799	0.96[ASN][1000 genomes]
rs11610714	0.96[ASN][1000 genomes]
rs12228207	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12229276	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12830701	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1866295	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2033774	0.95[AFR][1000 genomes]
rs34307072	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35371470	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35746861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35945096	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36034617	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3812803	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3935416	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4964289	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4964780	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4964794	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4964805	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4964806	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4964812	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4964823	0.81[AFR][1000 genomes]
rs67825151	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7134701	0.91[AMR][1000 genomes];0.94[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
rs4964623	RP11-341G23.4	cis	Thyroid	GTEx
rs4964623	RP11-341G23.4	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104208200-104223200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:104208200-104227800	Weak transcription	Pancreas	Pancrea
3	chr12:104208800-104227600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr12:104215200-104226000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:104215200-104227600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:104215400-104223400	Enhancers	Rectal Smooth Muscle	rectum
7	chr12:104216600-104227800	Weak transcription	NH-A	brain
8	chr12:104218400-104224800	Weak transcription	K562	blood
9	chr12:104218400-104233000	Weak transcription	Gastric	stomach
10	chr12:104218400-104233400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:104218800-104227400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:104218800-104232800	Weak transcription	Psoas Muscle	Psoas
13	chr12:104219600-104226400	Weak transcription	Ovary	ovary
14	chr12:104220000-104232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:104221200-104224200	Enhancers	Colon Smooth Muscle	Colon
16	chr12:104221400-104223400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr12:104221400-104223600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:104221400-104228200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr12:104221600-104223800	Enhancers	HepG2	liver
20	chr12:104221600-104224000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:104221600-104224000	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr12:104221800-104222800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:104221800-104223000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:104221800-104223600	Enhancers	NHEK	skin
25	chr12:104222000-104223200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:104222000-104223400	Enhancers	HMEC	breast
27	chr12:104222000-104224200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:104222000-104225800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:104222000-104226200	Enhancers	Primary B cells from cord blood	blood
30	chr12:104222200-104223200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:104222200-104223200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr12:104222200-104224800	Weak transcription	Aorta	Aorta
33	chr12:104222200-104226000	Weak transcription	Liver	Liver
34	chr12:104222200-104226200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:104222200-104226200	Weak transcription	Fetal Lung	lung
36	chr12:104222200-104226400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:104222200-104226600	Weak transcription	Brain Anterior Caudate	brain
38	chr12:104222200-104227400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:104222200-104232200	Weak transcription	NHLF	lung
40	chr12:104222400-104223000	Weak transcription	GM12878-XiMat	blood
41	chr12:104222400-104223000	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr12:104222400-104226400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:104222400-104226600	Weak transcription	Osteobl	bone
44	chr12:104222400-104227400	Weak transcription	HSMM	muscle
45	chr12:104222400-104228800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr12:104222600-104222800	Weak transcription	HSMMtube	muscle
47	chr12:104222600-104223000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr12:104222600-104223000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr12:104222600-104223200	Enhancers	Primary B cells from peripheral blood	blood
50	chr12:104222600-104232000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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