Variant report

Variant	rs57517202
Chromosome Location	chr2:55477086-55477087
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55475194..55477770-chr2:55494963..55497132,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085760	Chromatin interaction

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

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

rs_ID	r²[population]
rs11887112	0.82[AMR][1000 genomes]
rs11890896	0.91[AMR][1000 genomes]
rs17046771	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17046787	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55726603	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55735105	0.91[AMR][1000 genomes]
rs56219595	0.91[AMR][1000 genomes]
rs56887573	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56902676	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57489147	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58207828	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58485503	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59832517	0.82[AMR][1000 genomes]
rs61197615	0.82[AMR][1000 genomes]
rs6707902	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6716121	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6721728	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6723598	0.91[AMR][1000 genomes]
rs6724153	0.91[AMR][1000 genomes]
rs6736539	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73936949	0.91[AMR][1000 genomes]
rs73936959	0.91[AMR][1000 genomes]
rs73936964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7596403	0.91[AMR][1000 genomes]
rs7608709	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 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	chr2:55461400-55477600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55461600-55481600	Strong transcription	Fetal Thymus	thymus
3	chr2:55461600-55495400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:55461600-55495400	Weak transcription	Stomach Mucosa	stomach
5	chr2:55461800-55493400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:55461800-55495000	Weak transcription	Fetal Brain Male	brain
7	chr2:55462000-55493200	Strong transcription	Duodenum Mucosa	Duodenum
8	chr2:55462200-55490200	Weak transcription	Small Intestine	intestine
9	chr2:55462600-55485800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:55463000-55477600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr2:55463000-55480200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr2:55463000-55481000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:55463000-55495400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:55463200-55481000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:55463400-55488200	Weak transcription	Pancreas	Pancrea
16	chr2:55463600-55483800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:55463800-55479600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:55463800-55486200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:55463800-55490400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:55463800-55494800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:55463800-55495600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:55464400-55479600	Weak transcription	NHLF	lung
23	chr2:55464600-55479400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:55464600-55495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr2:55465400-55490600	Weak transcription	Brain Germinal Matrix	brain
26	chr2:55465600-55486000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr2:55465600-55494400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr2:55465800-55477600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:55466000-55493200	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr2:55468000-55477600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:55468200-55493400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr2:55468400-55493200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:55468400-55494400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:55468600-55494400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:55468800-55477600	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:55468800-55480400	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:55468800-55493600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:55468800-55494400	Strong transcription	Adipose Nuclei	Adipose
39	chr2:55468800-55494400	Strong transcription	Liver	Liver
40	chr2:55469000-55477200	Strong transcription	Stomach Smooth Muscle	stomach
41	chr2:55469000-55482000	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:55469400-55492600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr2:55469600-55481400	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr2:55469600-55481800	Strong transcription	Placenta	Placenta
45	chr2:55469800-55478000	Strong transcription	Primary T cells from cord blood	blood
46	chr2:55469800-55478600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr2:55470000-55481800	Strong transcription	A549	lung
48	chr2:55470600-55477400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:55470800-55494200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr2:55471000-55479400	Weak transcription	Brain Substantia Nigra	brain

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