Variant report

Variant	rs12744609
Chromosome Location	chr1:225997973-225997974
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:225997868..225998526-chr3:143572696..143573196,2	K562	blood:
2	chr1:225962862..225967352-chr1:225996084..226002774,11	MCF-7	breast:
3	chr1:225997762..225999546-chr1:226064729..226066981,2	MCF-7	breast:
4	chr1:225962294..225967531-chr1:225994011..226002080,11	K562	blood:
5	chr1:225997801..225999336-chr5:38846074..38848337,2	MCF-7	breast:
6	chr1:225997407..225998221-chr13:111367411..111367928,2	Hela-S3	cervix:
7	chr1:225963904..225970275-chr1:225994893..226001084,15	K562	blood:
8	chr1:225963814..225970754-chr1:225996230..226002908,14	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196187	Chromatin interaction
ENSG00000145623	Chromatin interaction
ENSG00000143742	Chromatin interaction
ENSG00000153487	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10737418	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10737419	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10737420	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10753409	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799323	0.82[EUR][1000 genomes]
rs10915877	0.87[EUR][1000 genomes]
rs10915878	0.97[ASN][1000 genomes]
rs11808973	0.86[EUR][1000 genomes]
rs12727007	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12741681	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12757220	0.82[EUR][1000 genomes]
rs1467143	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4559463	0.95[ASN][1000 genomes]
rs4653436	0.97[ASN][1000 genomes]
rs4653684	0.87[EUR][1000 genomes]
rs4653685	0.87[EUR][1000 genomes]
rs4653686	0.86[EUR][1000 genomes]
rs4653688	0.96[ASN][1000 genomes]
rs55736073	0.97[ASN][1000 genomes]
rs55954107	0.90[ASN][1000 genomes]
rs56195257	0.90[ASN][1000 genomes]
rs57440270	0.97[ASN][1000 genomes]
rs58241471	0.97[ASN][1000 genomes]
rs6426089	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6687036	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers 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	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv945327	chr1:225991086-225998770	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225986000-225998000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:225997200-225998000	Active TSS	HMEC	breast
3	chr1:225997200-225998400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:225997200-225998400	Active TSS	HSMMtube	muscle
5	chr1:225997200-225998600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:225997200-225998600	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:225997200-225998600	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr1:225997200-225998600	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr1:225997200-225998600	Active TSS	Hela-S3	cervix
10	chr1:225997200-225998600	Active TSS	HSMM	muscle
11	chr1:225997200-225998800	Active TSS	Osteobl	bone
12	chr1:225997200-225999000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:225997200-225999000	Active TSS	Brain Hippocampus Middle	brain
14	chr1:225997200-225999200	Active TSS	Brain Angular Gyrus	brain
15	chr1:225997200-225999200	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr1:225997200-225999200	Active TSS	Rectal Smooth Muscle	rectum
17	chr1:225997200-225999600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:225997400-225998000	Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr1:225997400-225998200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:225997400-225998200	Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr1:225997400-225998200	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr1:225997400-225998400	Active TSS	Primary T cells from cord blood	blood
23	chr1:225997400-225998400	Flanking Active TSS	Dnd41	blood
24	chr1:225997400-225998400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr1:225997400-225998600	Active TSS	H1 Cell Line	embryonic stem cell
26	chr1:225997400-225998600	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr1:225997400-225998600	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr1:225997400-225998600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:225997400-225998600	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr1:225997400-225998600	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr1:225997400-225998600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:225997400-225998600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:225997400-225998600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:225997400-225998600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:225997400-225998600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:225997400-225998600	Active TSS	Brain Substantia Nigra	brain
37	chr1:225997400-225998600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr1:225997400-225998600	Active TSS	Fetal Muscle Leg	muscle
39	chr1:225997400-225998600	Active TSS	Fetal Stomach	stomach
40	chr1:225997400-225998600	Active TSS	NH-A	brain
41	chr1:225997400-225998600	Active TSS	NHEK	skin
42	chr1:225997400-225998600	Active TSS	NHLF	lung
43	chr1:225997400-225998800	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr1:225997400-225998800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:225997400-225998800	Active TSS	Brain Anterior Caudate	brain
46	chr1:225997400-225998800	Active TSS	Colonic Mucosa	Colon
47	chr1:225997400-225998800	Active TSS	Psoas Muscle	Psoas
48	chr1:225997400-225998800	Active TSS	A549	lung
49	chr1:225997400-225999000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:225997400-225999000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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