Variant report

Variant	rs1727295
Chromosome Location	chr12:123616861-123616862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123464971..123468188-chr12:123616401..123619545,3	K562	blood:
2	chr12:123616297..123618408-chr12:123632574..123634282,2	MCF-7	breast:
3	chr12:123616804..123619547-chr12:123619557..123621511,2	K562	blood:
4	chr12:123606578..123609503-chr12:123615590..123618245,2	MCF-7	breast:
5	chr12:123616507..123619286-chr12:123631305..123632986,2	K562	blood:

Variant related genes	Relation type
ENSG00000182196	Chromatin interaction
ENSG00000150967	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10444439	0.81[JPT][hapmap]
rs1051434	0.95[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10773003	0.84[JPT][hapmap]
rs10773005	0.84[JPT][hapmap]
rs10773921	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap]
rs10846489	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs10848428	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11057251	0.84[JPT][hapmap];1.00[YRI][hapmap]
rs1109559	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs11608305	0.85[JPT][hapmap]
rs11608811	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap]
rs11610710	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11613128	0.87[AFR][1000 genomes]
rs12229700	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12317452	0.85[JPT][hapmap]
rs12366872	0.84[JPT][hapmap]
rs12425009	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap]
rs12425850	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs1568428	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs1611973	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1615350	0.90[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs1616484	0.85[AFR][1000 genomes]
rs1716178	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1716184	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1727286	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1727293	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1727301	0.85[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1727302	0.90[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs1727305	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1727307	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1727312	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1790088	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1790094	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1790096	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1790104	0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1790106	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1790121	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1790122	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1790129	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1790134	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1879379	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2337630	0.82[AFR][1000 genomes]
rs2337631	0.82[AFR][1000 genomes]
rs2682427	0.85[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs3088303	0.84[JPT][hapmap]
rs34841857	0.82[AFR][1000 genomes]
rs3741530	0.87[CEU][hapmap]
rs3759115	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap]
rs3897102	0.95[CHB][hapmap]
rs4148862	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4148863	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4275659	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap]
rs4759377	0.84[JPT][hapmap]
rs58991895	0.80[ASN][1000 genomes]
rs6488868	0.82[CEU][hapmap]
rs7135296	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap]
rs7139321	0.80[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7296418	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs7305511	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap]
rs7957096	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs884956	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs949143	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv870326	chr12:123585990-123719323	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	esv2761773	chr12:123616003-123723460	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1727295	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs1727295	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1727295	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1727295	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1727295	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1727295	SETD8	Cis_1M	lymphoblastoid	RTeQTL
rs1727295	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1727295	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123594600-123634000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:123599200-123624600	Weak transcription	Fetal Brain Female	brain
3	chr12:123605800-123624400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:123607600-123619600	Genic enhancers	Fetal Thymus	thymus
5	chr12:123610000-123620400	Enhancers	Placenta	Placenta
6	chr12:123611000-123617400	Enhancers	Primary B cells from cord blood	blood
7	chr12:123611400-123624400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:123611600-123617400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:123611800-123618000	Enhancers	A549	lung
10	chr12:123611800-123624400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:123611800-123624400	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:123611800-123624600	Weak transcription	Aorta	Aorta
13	chr12:123612000-123617400	Weak transcription	HepG2	liver
14	chr12:123612000-123618600	Weak transcription	Fetal Intestine Small	intestine
15	chr12:123612000-123624000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:123612000-123624600	Weak transcription	NH-A	brain
17	chr12:123613600-123620400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:123614000-123617000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:123614000-123619200	Enhancers	NHEK	skin
20	chr12:123614200-123618000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr12:123614200-123620400	Enhancers	HMEC	breast
22	chr12:123614600-123618000	Enhancers	NHDF-Ad	bronchial
23	chr12:123614800-123617000	Enhancers	Fetal Muscle Trunk	muscle
24	chr12:123614800-123617000	Enhancers	Left Ventricle	heart
25	chr12:123614800-123618000	Enhancers	Fetal Muscle Leg	muscle
26	chr12:123614800-123618200	Enhancers	Dnd41	blood
27	chr12:123615000-123617600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr12:123615200-123617800	Enhancers	Fetal Heart	heart
29	chr12:123615200-123618200	Enhancers	Esophagus	oesophagus
30	chr12:123615400-123617000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:123615400-123617000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:123615400-123617000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:123615400-123617000	Enhancers	Lung	lung
34	chr12:123615400-123617000	Enhancers	Placenta Amnion	Placenta Amnion
35	chr12:123615400-123617000	Enhancers	Hela-S3	cervix
36	chr12:123615400-123617600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:123615400-123618000	Enhancers	HSMM	muscle
38	chr12:123615400-123620200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:123615600-123617000	Enhancers	Right Ventricle	heart
40	chr12:123615600-123617400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr12:123615600-123618000	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr12:123615800-123617000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:123615800-123617000	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr12:123615800-123617000	Enhancers	Muscle Satellite Cultured Cells	--
45	chr12:123615800-123617000	Enhancers	Pancreas	Pancrea
46	chr12:123615800-123617000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr12:123615800-123617200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:123615800-123617600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:123615800-123618200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:123615800-123618200	Enhancers	Colon Smooth Muscle	Colon

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