Variant report

Variant	rs12405120
Chromosome Location	chr1:84556523-84556524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:84541438..84545739-chr1:84555567..84558104,4	K562	blood:
2	chr1:84553847..84557736-chr1:84560723..84565476,4	K562	blood:
3	chr1:84551652..84556823-chr1:84558383..84561144,5	K562	blood:
4	chr1:84549201..84550901-chr1:84554947..84556654,2	K562	blood:
5	chr1:84556236..84558984-chr1:84559547..84561523,2	MCF-7	breast:
6	chr1:84554743..84559247-chr1:84561300..84565476,7	K562	blood:

Variant related genes	Relation type
ENSG00000271576	Chromatin interaction
ENSG00000142875	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1021490	0.82[AMR][1000 genomes]
rs10493750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1057738	0.85[GIH][hapmap]
rs11163897	0.80[JPT][hapmap]
rs11163898	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11163900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163905	0.81[GIH][hapmap]
rs11163906	0.81[GIH][hapmap];0.83[MEX][hapmap]
rs11163907	0.81[GIH][hapmap]
rs12070547	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12119275	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs12132032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12404263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12724598	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12746741	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12748859	0.83[ASW][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap]
rs12750691	0.84[AMR][1000 genomes]
rs1402694	0.81[GIH][hapmap]
rs1521518	0.81[GIH][hapmap];0.83[MEX][hapmap]
rs1565823	0.88[GIH][hapmap];0.83[MEX][hapmap];0.86[AMR][1000 genomes]
rs2037454	0.88[GIH][hapmap]
rs2134647	0.84[GIH][hapmap]
rs2134648	0.83[ASW][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap]
rs34179759	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34495740	0.93[ASN][1000 genomes]
rs35452337	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3861699	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs6576962	0.81[GIH][hapmap]
rs6669045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674038	0.80[JPT][hapmap]
rs6696125	0.88[GIH][hapmap]
rs6703653	0.90[JPT][hapmap]
rs67276144	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72711192	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515976	0.88[GIH][hapmap];0.83[MEX][hapmap]
rs7520283	0.90[JPT][hapmap]
rs953197	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs957828	0.80[JPT][hapmap]
rs970318	0.81[ASW][hapmap];0.88[GIH][hapmap]

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	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12405120	PRKACB	cis	lymphoblastoid	seeQTL
rs12405120	BCL10	cis	cerebellum	SCAN
rs12405120	MCOLN2	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84544600-84557200	Weak transcription	Gastric	stomach
2	chr1:84545000-84557200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:84545000-84558800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:84545000-84560600	Weak transcription	Fetal Lung	lung
5	chr1:84545000-84561200	Weak transcription	Ovary	ovary
6	chr1:84545000-84566800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:84545000-84570000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:84545200-84568600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:84545400-84560800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:84545800-84568600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:84546400-84560400	Weak transcription	Dnd41	blood
12	chr1:84552200-84558600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:84552200-84561800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:84552200-84561800	Weak transcription	Right Atrium	heart
15	chr1:84552200-84569000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:84552400-84557200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:84552600-84562000	Weak transcription	Fetal Stomach	stomach
18	chr1:84554400-84556600	Enhancers	Hela-S3	cervix
19	chr1:84554400-84556600	Enhancers	HMEC	breast
20	chr1:84554600-84556600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:84554600-84556600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:84554600-84556800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:84554600-84560000	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:84554800-84556600	Enhancers	NHEK	skin
25	chr1:84554800-84556600	Enhancers	NHLF	lung
26	chr1:84554800-84556600	Enhancers	Osteobl	bone
27	chr1:84555000-84556800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr1:84555000-84557000	Enhancers	Fetal Intestine Small	intestine
29	chr1:84555000-84557200	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr1:84555400-84558200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr1:84555400-84559800	Weak transcription	NH-A	brain
32	chr1:84555400-84568400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:84555600-84557000	Enhancers	Fetal Intestine Large	intestine
34	chr1:84556000-84556600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr1:84556000-84556600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr1:84556000-84557000	Enhancers	Stomach Mucosa	stomach
37	chr1:84556000-84557200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:84556200-84556600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:84556200-84556600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:84556200-84556600	Enhancers	Small Intestine	intestine
41	chr1:84556200-84556800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr1:84556200-84556800	Flanking Active TSS	Liver	Liver
43	chr1:84556200-84557000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:84556200-84557000	Active TSS	Duodenum Mucosa	Duodenum
45	chr1:84556200-84557000	Active TSS	Monocytes-CD14+_RO01746	blood
46	chr1:84556200-84557200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:84556200-84557200	Flanking Active TSS	GM12878-XiMat	blood
48	chr1:84556200-84557400	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr1:84556400-84556600	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr1:84556400-84556600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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