Variant report

Variant	rs1727305
Chromosome Location	chr12:123633382-123633383
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123625936..123634145-chr12:123634916..123640513,10	K562	blood:
2	chr12:123624513..123626615-chr12:123631268..123633682,3	K562	blood:
3	chr12:123632948..123634613-chr12:123717747..123719847,2	K562	blood:
4	chr12:123633130..123634910-chr12:123716201..123717715,2	K562	blood:
5	chr12:123633368..123635688-chr12:123701614..123704544,2	MCF-7	breast:
6	chr12:123616297..123618408-chr12:123632574..123634282,2	MCF-7	breast:
7	chr12:123603146..123605205-chr12:123632203..123634341,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000130921	Chromatin interaction
ENSG00000051825	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1051434	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10846489	0.82[AFR][1000 genomes]
rs10848428	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11057219	0.82[AFR][1000 genomes]
rs1109559	0.82[AFR][1000 genomes]
rs11610710	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11613128	0.87[AFR][1000 genomes]
rs12229700	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1568428	0.84[AFR][1000 genomes]
rs1611973	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1615350	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1616484	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1626703	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1716178	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1716184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1727286	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1727293	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1727295	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1727301	0.87[ASN][1000 genomes]
rs1727302	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1727307	0.87[EUR][1000 genomes]
rs1727312	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1790088	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1790094	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1790096	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1790104	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1790106	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1790121	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1790122	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1790129	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1790134	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1879379	0.82[AFR][1000 genomes]
rs2337630	0.82[AFR][1000 genomes]
rs2337631	0.82[AFR][1000 genomes]
rs2682427	0.87[ASN][1000 genomes]
rs34841857	0.82[AFR][1000 genomes]
rs4148862	0.88[EUR][1000 genomes]
rs4148863	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4553407	0.82[AFR][1000 genomes]
rs58991895	0.83[ASN][1000 genomes]
rs61041384	0.82[ASN][1000 genomes]
rs61187102	0.80[ASN][1000 genomes]
rs7139321	0.87[AFR][1000 genomes]
rs949143	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1727305	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1727305	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1727305	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1727305	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1727305	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1727305	CDK2AP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123594600-123634000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:123618000-123634200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:123625000-123633600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:123625400-123633800	Weak transcription	Fetal Brain Male	brain
5	chr12:123625400-123634600	Weak transcription	Aorta	Aorta
6	chr12:123627000-123634200	Weak transcription	NHEK	skin
7	chr12:123627000-123634800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:123627200-123634000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:123627200-123634000	Weak transcription	HMEC	breast
10	chr12:123627200-123634000	Weak transcription	HSMMtube	muscle
11	chr12:123627800-123633600	Weak transcription	Stomach Mucosa	stomach
12	chr12:123627800-123633800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:123627800-123634000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr12:123627800-123634400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:123628000-123633400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:123628000-123633600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:123628000-123633600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:123628000-123633600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr12:123628000-123634200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:123628200-123633400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr12:123628200-123633400	Weak transcription	Fetal Intestine Large	intestine
22	chr12:123628200-123633600	Weak transcription	Fetal Intestine Small	intestine
23	chr12:123628200-123633800	Weak transcription	Fetal Stomach	stomach
24	chr12:123628400-123633400	Weak transcription	Placenta	Placenta
25	chr12:123628400-123633600	Weak transcription	Psoas Muscle	Psoas
26	chr12:123628400-123633800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:123628400-123634000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:123628600-123633400	Weak transcription	Gastric	stomach
29	chr12:123628600-123633600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:123628600-123633600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr12:123628600-123633800	Weak transcription	Adipose Nuclei	Adipose
32	chr12:123628600-123634000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:123628800-123633400	Weak transcription	Brain Substantia Nigra	brain
34	chr12:123628800-123633800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr12:123628800-123633800	Weak transcription	NHLF	lung
36	chr12:123628800-123634400	Weak transcription	Esophagus	oesophagus
37	chr12:123629000-123633600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:123629000-123633600	Weak transcription	NHDF-Ad	bronchial
39	chr12:123629000-123633800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:123629000-123633800	Weak transcription	Colon Smooth Muscle	Colon
41	chr12:123629000-123633800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:123629000-123633800	Weak transcription	NH-A	brain
43	chr12:123629000-123634200	Weak transcription	Osteobl	bone
44	chr12:123629200-123633400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:123630400-123633400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr12:123630400-123633600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr12:123630400-123633800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr12:123630400-123633800	Weak transcription	A549	lung
49	chr12:123630600-123633600	Weak transcription	Hela-S3	cervix
50	chr12:123630600-123633800	Weak transcription	Fetal Kidney	kidney

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