Variant report

Variant	rs28600892
Chromosome Location	chr2:20782140-20782141
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20723966..20726064-chr2:20781037..20784035,2	K562	blood:
2	chr2:20644778..20652349-chr2:20775724..20782509,25	MCF-7	breast:
3	chr2:20666244..20668102-chr2:20780641..20782440,2	MCF-7	breast:
4	chr2:20772999..20776929-chr2:20778925..20783592,5	MCF-7	breast:
5	chr2:20778242..20781356-chr2:20782083..20785108,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228950	Chromatin interaction
ENSG00000143878	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10176721	0.85[AMR][1000 genomes]
rs10200826	0.85[AMR][1000 genomes]
rs28488411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28529647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28642817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55751815	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55793738	0.92[AFR][1000 genomes]
rs57360378	0.88[AFR][1000 genomes]
rs57494499	0.85[AMR][1000 genomes]
rs57524662	0.85[AMR][1000 genomes]
rs58590712	0.85[AMR][1000 genomes]
rs58696000	0.85[AMR][1000 genomes]
rs58726406	0.90[AFR][1000 genomes]
rs59300971	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59618840	0.90[AFR][1000 genomes]
rs59771803	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59882809	0.85[AMR][1000 genomes]
rs60283906	0.85[AMR][1000 genomes]
rs60759855	0.92[AFR][1000 genomes]
rs61272752	0.92[AFR][1000 genomes]
rs61478003	0.85[AMR][1000 genomes]
rs62124225	0.93[AFR][1000 genomes]
rs62124226	0.93[AFR][1000 genomes]
rs62124227	0.93[AFR][1000 genomes]
rs62124228	0.93[AFR][1000 genomes]
rs62124229	0.93[AFR][1000 genomes]
rs62124230	0.93[AFR][1000 genomes]
rs62124231	0.93[AFR][1000 genomes]
rs62124232	0.93[AFR][1000 genomes]
rs62124234	0.90[AFR][1000 genomes]
rs73235057	0.85[AMR][1000 genomes]
rs73235060	0.85[AMR][1000 genomes]
rs73235063	0.85[AMR][1000 genomes]
rs73235064	0.85[AMR][1000 genomes]
rs73235072	0.85[AMR][1000 genomes]
rs73235100	0.85[AMR][1000 genomes]
rs73237114	0.85[AMR][1000 genomes]
rs73237135	0.85[AMR][1000 genomes]
rs73919913	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73919915	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73919918	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73919920	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73919921	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73919922	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73919923	0.93[AFR][1000 genomes]
rs73919924	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73919926	0.86[AFR][1000 genomes]
rs73919928	0.93[AFR][1000 genomes]
rs73919930	0.82[AFR][1000 genomes]
rs7564684	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7574045	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7574289	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7588678	0.89[AFR][1000 genomes]
rs7601273	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20765800-20786200	Enhancers	HUVEC	blood vessel
2	chr2:20767800-20782600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:20772600-20785800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:20778800-20784800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:20779000-20782400	Weak transcription	Pancreas	Pancrea
6	chr2:20779000-20782800	Weak transcription	Gastric	stomach
7	chr2:20779600-20783600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:20779600-20783800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:20779800-20783600	Weak transcription	Fetal Kidney	kidney
10	chr2:20779800-20783800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:20779800-20784000	Enhancers	HepG2	liver
12	chr2:20780000-20782400	Weak transcription	Fetal Intestine Large	intestine
13	chr2:20780000-20782400	Weak transcription	Right Ventricle	heart
14	chr2:20780000-20783600	Weak transcription	Osteobl	bone
15	chr2:20780000-20783800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:20780000-20783800	Weak transcription	Ovary	ovary
17	chr2:20780000-20784000	Weak transcription	Aorta	Aorta
18	chr2:20780000-20784200	Weak transcription	Psoas Muscle	Psoas
19	chr2:20780000-20784200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr2:20780000-20784400	Weak transcription	Colonic Mucosa	Colon
21	chr2:20780000-20786000	Weak transcription	Small Intestine	intestine
22	chr2:20780200-20782200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:20780200-20783400	Weak transcription	NHDF-Ad	bronchial
24	chr2:20780800-20782600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:20780800-20782600	Weak transcription	NHLF	lung
26	chr2:20780800-20782800	Weak transcription	Fetal Heart	heart
27	chr2:20780800-20783600	Weak transcription	Colon Smooth Muscle	Colon
28	chr2:20780800-20784000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:20781000-20782400	Weak transcription	Left Ventricle	heart
30	chr2:20781000-20782400	Weak transcription	Right Atrium	heart
31	chr2:20781000-20782600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:20781000-20782600	Weak transcription	Stomach Mucosa	stomach
33	chr2:20781000-20782600	Weak transcription	Hela-S3	cervix
34	chr2:20781000-20782800	Weak transcription	Lung	lung
35	chr2:20781200-20784200	Weak transcription	Liver	Liver
36	chr2:20781400-20782200	ZNF genes & repeats	Placenta	Placenta
37	chr2:20781400-20782200	ZNF genes & repeats	Fetal Stomach	stomach
38	chr2:20781400-20782200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
39	chr2:20781600-20785400	Enhancers	Placenta Amnion	Placenta Amnion
40	chr2:20781600-20786000	Enhancers	Brain Hippocampus Middle	brain
41	chr2:20781800-20782200	Weak transcription	Adipose Nuclei	Adipose
42	chr2:20781800-20782200	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr2:20781800-20782400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:20781800-20786000	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr2:20781800-20786000	Enhancers	Brain Anterior Caudate	brain
46	chr2:20781800-20786000	Enhancers	Brain Substantia Nigra	brain
47	chr2:20781800-20786200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:20781800-20786800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:20782000-20782200	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr2:20782000-20782400	Flanking Active TSS	Brain Cingulate Gyrus	brain

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