Variant report

Variant	rs4964629
Chromosome Location	chr12:104221850-104221851
allele	A/G
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	chr12:104214519..104222192-chr12:104231005..104236989,8	K562	blood:
3	chr12:104219162..104221997-chr12:104232338..104234895,2	K562	blood:
4	chr12:104221570..104225596-chr12:104232317..104237466,6	MCF-7	breast:
5	chr12:104221267..104222834-chr12:104227996..104230491,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257327	Chromatin interaction
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10735389	0.83[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs10778286	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs10778290	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861106	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861107	0.85[CHB][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs10861112	0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111774	0.93[ASN][1000 genomes]
rs11111801	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12307138	0.85[CHB][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs12425205	0.85[CHB][hapmap];0.87[CHD][hapmap];0.89[ASN][1000 genomes]
rs1973658	0.91[ASN][1000 genomes]
rs3812804	0.85[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs4248827	0.93[ASN][1000 genomes]
rs4300459	0.86[ASW][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs4964818	0.90[ASN][1000 genomes]
rs4981034	0.83[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6539101	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs7135173	0.91[ASN][1000 genomes]
rs7136682	1.00[CHD][hapmap];0.83[JPT][hapmap]
rs7970553	0.85[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs9739384	0.91[JPT][hapmap];0.91[ASN][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
rs4964629	APPL2	cis	parietal	SCAN
rs4964629	TU12B1-TY	cis	multi-tissue	Pritchard

Chromatin state (count:58 , 50 per page) page: 1 2

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	chr12:104217800-104222000	Weak transcription	Fetal Muscle Leg	muscle
9	chr12:104218400-104224800	Weak transcription	K562	blood
10	chr12:104218400-104233000	Weak transcription	Gastric	stomach
11	chr12:104218400-104233400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:104218800-104227400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:104218800-104232800	Weak transcription	Psoas Muscle	Psoas
14	chr12:104219000-104222000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:104219600-104226400	Weak transcription	Ovary	ovary
16	chr12:104220000-104232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:104220400-104222000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:104220600-104222600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr12:104221200-104222000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:104221200-104222200	Enhancers	A549	lung
21	chr12:104221200-104224200	Enhancers	Colon Smooth Muscle	Colon
22	chr12:104221400-104222200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:104221400-104222200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:104221400-104223400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr12:104221400-104223600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:104221400-104228200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr12:104221600-104222000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:104221600-104222000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr12:104221600-104222000	Flanking Active TSS	HMEC	breast
30	chr12:104221600-104222200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:104221600-104222200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:104221600-104222200	Enhancers	NHLF	lung
33	chr12:104221600-104222400	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr12:104221600-104222400	Enhancers	GM12878-XiMat	blood
35	chr12:104221600-104222400	Enhancers	HSMM	muscle
36	chr12:104221600-104222400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr12:104221600-104222400	Enhancers	NHDF-Ad	bronchial
38	chr12:104221600-104223800	Enhancers	HepG2	liver
39	chr12:104221600-104224000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:104221600-104224000	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr12:104221800-104222000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:104221800-104222000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:104221800-104222000	Enhancers	Brain Angular Gyrus	brain
44	chr12:104221800-104222200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:104221800-104222200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:104221800-104222200	Enhancers	Aorta	Aorta
47	chr12:104221800-104222200	Enhancers	Liver	Liver
48	chr12:104221800-104222200	Enhancers	Brain Anterior Caudate	brain
49	chr12:104221800-104222200	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr12:104221800-104222200	Enhancers	Fetal Lung	lung

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