Variant report

Variant	rs56097129
Chromosome Location	chr2:112687239-112687240
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:112687076..112688579-chr2:112812009..112814430,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153214	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11123024	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11681295	0.81[ASN][1000 genomes]
rs1996329	0.81[ASN][1000 genomes]
rs1996330	0.81[ASN][1000 genomes]
rs28637361	0.81[ASN][1000 genomes]
rs4468823	0.81[ASN][1000 genomes]
rs4848908	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56822761	0.84[ASN][1000 genomes]
rs59219838	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62162478	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62162480	0.83[ASN][1000 genomes]
rs67063370	0.81[ASN][1000 genomes]
rs7569614	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1801950	chr2:111899783-112746937	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	esv2757825	chr2:111899783-112746937	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	esv2759083	chr2:111899783-112746937	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
7	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv998028	chr2:112649472-112734015	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv582701	chr2:112649472-112740597	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv526647	chr2:112651316-112738562	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv582702	chr2:112651316-112738562	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	esv3333591	chr2:112669320-112892618	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv1002027	chr2:112679182-112861534	Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv1014787	chr2:112679182-112908416	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv535893	chr2:112679182-112908416	Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112664600-112687600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr2:112664600-112702200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:112666400-112692800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:112674600-112687400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:112674800-112687600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:112676400-112702200	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:112677800-112697800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:112678000-112687600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:112678000-112688600	Weak transcription	A549	lung
10	chr2:112678000-112690600	Weak transcription	Small Intestine	intestine
11	chr2:112678000-112691200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:112678000-112705600	Weak transcription	Esophagus	oesophagus
13	chr2:112678200-112687600	Weak transcription	Adipose Nuclei	Adipose
14	chr2:112678800-112689800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:112682400-112687600	Weak transcription	Aorta	Aorta
16	chr2:112682400-112687800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:112682400-112703200	Weak transcription	Placenta	Placenta
18	chr2:112683200-112703200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:112683400-112698600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:112684400-112688400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:112684600-112703000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:112684800-112687600	Weak transcription	Spleen	Spleen
23	chr2:112684800-112705200	Weak transcription	Fetal Muscle Leg	muscle
24	chr2:112685000-112687600	Weak transcription	Brain Substantia Nigra	brain
25	chr2:112685000-112687600	Weak transcription	Left Ventricle	heart
26	chr2:112685000-112688000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr2:112685000-112688800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:112685000-112690400	Weak transcription	Stomach Mucosa	stomach
29	chr2:112685000-112694400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr2:112685000-112702200	Weak transcription	Pancreas	Pancrea
31	chr2:112685200-112687800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:112685400-112688000	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:112685600-112687600	Weak transcription	Brain Anterior Caudate	brain
34	chr2:112685600-112688200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:112685600-112694200	Weak transcription	Brain Angular Gyrus	brain
36	chr2:112685600-112694600	Weak transcription	Right Atrium	heart
37	chr2:112685600-112703200	Weak transcription	Right Ventricle	heart
38	chr2:112686200-112689400	Strong transcription	Fetal Intestine Small	intestine
39	chr2:112686200-112689600	Strong transcription	Stomach Smooth Muscle	stomach
40	chr2:112686400-112688200	Strong transcription	HUVEC	blood vessel
41	chr2:112686400-112689000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:112686400-112693000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:112686600-112688200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:112686600-112688200	Strong transcription	Ovary	ovary
45	chr2:112686600-112688600	Strong transcription	Lung	lung
46	chr2:112686600-112688600	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr2:112686600-112689600	Strong transcription	Fetal Stomach	stomach
48	chr2:112686600-112689600	Strong transcription	HepG2	liver
49	chr2:112686600-112689800	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:112686600-112691000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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