Variant report

Variant	rs6542067
Chromosome Location	chr2:113380619-113380620
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr2:113379917-113380662	SK-N-SH	brain:	n/a	n/a
2	PBX3	chr2:113379856-113380633	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr2:113379274-113380652	SK-N-SH	brain:	n/a	n/a
4	EP300	chr2:113379817-113380650	SK-N-SH	brain:	n/a	chr2:113380363-113380377
5	TCF12	chr2:113379837-113380684	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr2:113378650-113380668	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr2:113378904-113380703	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:113379636..113386577-chr2:113398111..113406278,16	MCF-7	breast:
2	chr2:113380240..113386960-chr2:113401832..113406779,10	MCF-7	breast:
3	chr2:113380065..113382456-chr2:113480700..113483703,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231747	TF binding region
ENSG00000144136	Chromatin interaction
ENSG00000237753	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11680446	0.89[EUR][1000 genomes]
rs3088301	0.97[ASN][1000 genomes]
rs35743012	0.97[ASN][1000 genomes]
rs3849316	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3849317	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3980075	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4547533	0.81[ASN][1000 genomes]
rs4848284	0.95[ASN][1000 genomes]
rs4849078	0.92[ASN][1000 genomes]
rs4849079	0.96[ASN][1000 genomes]
rs4849083	0.95[ASN][1000 genomes]
rs6542065	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6542066	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6542068	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6740202	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6758898	0.95[ASN][1000 genomes]
rs7559385	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	nsv963705	chr2:113379400-113381483	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113348600-113383600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:113349000-113384000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:113357800-113384200	Weak transcription	Pancreas	Pancrea
4	chr2:113358000-113384000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:113370400-113383800	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:113371600-113382000	Weak transcription	Spleen	Spleen
7	chr2:113372200-113384200	Weak transcription	Fetal Intestine Small	intestine
8	chr2:113372400-113384000	Weak transcription	Brain Anterior Caudate	brain
9	chr2:113372400-113388600	Weak transcription	Gastric	stomach
10	chr2:113372800-113388000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:113373000-113383200	Weak transcription	Fetal Brain Female	brain
12	chr2:113373200-113384000	Weak transcription	Brain Germinal Matrix	brain
13	chr2:113377400-113384200	Weak transcription	Right Atrium	heart
14	chr2:113378200-113382000	Weak transcription	Adipose Nuclei	Adipose
15	chr2:113378400-113382200	Enhancers	HMEC	breast
16	chr2:113378600-113381600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:113378800-113382000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:113378800-113384000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:113379800-113384200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr2:113379800-113387600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:113380000-113381600	Weak transcription	Esophagus	oesophagus
22	chr2:113380000-113381800	Enhancers	Hela-S3	cervix
23	chr2:113380000-113382000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:113380000-113382200	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr2:113380000-113384000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr2:113380200-113381600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:113380200-113381600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:113380200-113381600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:113380200-113381600	Weak transcription	Placenta	Placenta
30	chr2:113380200-113381600	Weak transcription	A549	lung
31	chr2:113380200-113381600	Weak transcription	NHDF-Ad	bronchial
32	chr2:113380200-113381600	Enhancers	NHEK	skin
33	chr2:113380200-113381800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr2:113380200-113381800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:113380200-113381800	Enhancers	Muscle Satellite Cultured Cells	--
36	chr2:113380200-113381800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:113380200-113382000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:113380200-113382000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:113380200-113382400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr2:113380200-113387600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr2:113380400-113381000	Weak transcription	NHLF	lung
42	chr2:113380400-113381400	Weak transcription	HUVEC	blood vessel
43	chr2:113380400-113381600	Weak transcription	HSMMtube	muscle
44	chr2:113380400-113382000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr2:113380400-113384200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr2:113380400-113387600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr2:113380600-113381600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:113380600-113381600	Weak transcription	K562	blood
49	chr2:113380600-113381600	Weak transcription	NH-A	brain
50	chr2:113380600-113381800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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