Variant report

Variant	rs55780001
Chromosome Location	chr2:10112699-10112700
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10102444..10109047-chr2:10109192..10115495,9	MCF-7	breast:
2	chr2:10111585..10113356-chr2:10123202..10126710,3	K562	blood:
3	chr2:10105826..10108731-chr2:10110445..10113153,2	K562	blood:
4	chr2:10109306..10112948-chr2:10113189..10116781,5	MCF-7	breast:
5	chr2:10090548..10095647-chr2:10110720..10115558,5	MCF-7	breast:
6	chr2:10090250..10093240-chr2:10111016..10113774,2	K562	blood:
7	chr2:9984016..9986818-chr2:10112280..10114129,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134317	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11884250	1.00[ASN][1000 genomes]
rs11888501	1.00[ASN][1000 genomes]
rs11893694	1.00[ASN][1000 genomes]
rs11902268	1.00[ASN][1000 genomes]
rs11902457	1.00[ASN][1000 genomes]
rs1367383	0.81[AFR][1000 genomes]
rs16867251	1.00[ASN][1000 genomes]
rs16867254	1.00[ASN][1000 genomes]
rs16867256	1.00[ASN][1000 genomes]
rs16867257	1.00[ASN][1000 genomes]
rs16867261	1.00[ASN][1000 genomes]
rs2011523	0.83[AFR][1000 genomes]
rs41264185	1.00[ASN][1000 genomes]
rs41264203	1.00[ASN][1000 genomes]
rs4496316	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4610026	0.81[AFR][1000 genomes]
rs4613247	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59658303	1.00[ASN][1000 genomes]
rs60026782	1.00[ASN][1000 genomes]
rs61221335	1.00[ASN][1000 genomes]
rs6432048	0.81[AFR][1000 genomes]
rs6726950	1.00[ASN][1000 genomes]
rs6730919	1.00[ASN][1000 genomes]
rs6731160	1.00[ASN][1000 genomes]
rs6733974	1.00[ASN][1000 genomes]
rs6734239	1.00[ASN][1000 genomes]
rs6735658	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6741117	1.00[ASN][1000 genomes]
rs6744044	1.00[ASN][1000 genomes]
rs6744047	1.00[ASN][1000 genomes]
rs6754701	1.00[ASN][1000 genomes]
rs731453	0.81[AFR][1000 genomes]
rs73913930	1.00[ASN][1000 genomes]
rs7601896	1.00[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	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv828297	chr2:10109299-10236332	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription 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 miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10092600-10113400	Weak transcription	Left Ventricle	heart
2	chr2:10094800-10124400	Weak transcription	Fetal Intestine Large	intestine
3	chr2:10099000-10115400	Strong transcription	Liver	Liver
4	chr2:10101000-10113200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:10101000-10117000	Strong transcription	HepG2	liver
6	chr2:10101400-10144800	Weak transcription	Brain Germinal Matrix	brain
7	chr2:10101600-10113000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:10101600-10116400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:10101600-10136400	Weak transcription	Brain Angular Gyrus	brain
10	chr2:10101800-10114800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:10102200-10136400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:10102400-10116600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:10104600-10130200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:10106000-10119800	Weak transcription	Dnd41	blood
15	chr2:10109400-10115600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:10109600-10112800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:10109600-10112800	Weak transcription	Fetal Thymus	thymus
18	chr2:10110200-10117800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:10110400-10113200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:10110400-10113400	Enhancers	Ovary	ovary
21	chr2:10110400-10113600	Enhancers	Placenta Amnion	Placenta Amnion
22	chr2:10110400-10115200	Bivalent Enhancer	Fetal Lung	lung
23	chr2:10110400-10116200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:10110600-10114000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:10110600-10117200	Enhancers	NHDF-Ad	bronchial
26	chr2:10110800-10113600	Enhancers	Placenta	Placenta
27	chr2:10111000-10112800	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:10111000-10113600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:10111000-10113600	Enhancers	NHEK	skin
30	chr2:10111000-10114800	Weak transcription	Colon Smooth Muscle	Colon
31	chr2:10111000-10116200	Weak transcription	Adipose Nuclei	Adipose
32	chr2:10111000-10117000	Enhancers	NHLF	lung
33	chr2:10111200-10113800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:10111200-10116000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:10111200-10116400	Weak transcription	Psoas Muscle	Psoas
36	chr2:10111400-10113000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:10111400-10113400	Weak transcription	Right Atrium	heart
38	chr2:10111400-10115800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:10111800-10112800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:10112000-10113400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:10112000-10113600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:10112200-10113400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:10112200-10113600	Enhancers	HMEC	breast
44	chr2:10112400-10113600	Enhancers	Stomach Mucosa	stomach
45	chr2:10112400-10113800	Enhancers	Fetal Kidney	kidney
46	chr2:10112600-10113000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:10112600-10113400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:10112600-10113400	Enhancers	Fetal Intestine Small	intestine
49	chr2:10112600-10113400	Genic enhancers	Lung	lung
50	chr2:10112600-10113600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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