Variant report

Variant	rs16823948
Chromosome Location	chr2:183898944-183898945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:183888564..183890207-chr2:183897911..183900162,2	MCF-7	breast:
2	chr2:183897885..183903273-chr2:183986817..183992325,13	K562	blood:
3	chr2:183895298..183904606-chr2:183986062..183992067,16	K562	blood:
4	chr2:183871994..183874914-chr2:183897971..183902484,5	MCF-7	breast:
5	chr2:183897393..183900215-chr2:183986353..183991181,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163002	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11885629	0.88[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11885833	1.00[EUR][1000 genomes]
rs11888086	1.00[EUR][1000 genomes]
rs11892717	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11896088	1.00[EUR][1000 genomes]
rs11903791	0.82[YRI][hapmap]
rs16823829	1.00[EUR][1000 genomes]
rs16823945	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16823949	1.00[EUR][1000 genomes]
rs16823966	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs16823968	0.89[YRI][hapmap];0.92[AFR][1000 genomes]
rs2102770	0.89[YRI][hapmap];0.92[AFR][1000 genomes]
rs4358084	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55803212	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55886059	1.00[EUR][1000 genomes]
rs56179717	1.00[EUR][1000 genomes]
rs56344408	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56362542	1.00[EUR][1000 genomes]
rs57047150	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58515193	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59253255	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59308931	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60558126	1.00[EUR][1000 genomes]
rs60602756	1.00[EUR][1000 genomes]
rs60705462	0.82[AFR][1000 genomes]
rs6733333	1.00[EUR][1000 genomes]
rs6736252	1.00[EUR][1000 genomes]
rs6757286	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73035662	0.82[AFR][1000 genomes]
rs73037284	1.00[EUR][1000 genomes]
rs73040079	1.00[EUR][1000 genomes]
rs73040083	1.00[EUR][1000 genomes]
rs73040085	1.00[EUR][1000 genomes]
rs73040088	1.00[EUR][1000 genomes]
rs73042107	1.00[EUR][1000 genomes]
rs73042129	1.00[EUR][1000 genomes]
rs73042136	1.00[EUR][1000 genomes]
rs73042149	1.00[EUR][1000 genomes]
rs73042166	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73046211	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73046213	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73046217	1.00[EUR][1000 genomes]
rs73046218	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73046222	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73046226	1.00[EUR][1000 genomes]
rs73046232	1.00[EUR][1000 genomes]
rs73046235	1.00[EUR][1000 genomes]
rs73046257	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73046260	1.00[EUR][1000 genomes]
rs73048203	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73980523	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73980527	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7558834	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7561870	1.00[EUR][1000 genomes]
rs7584932	1.00[EUR][1000 genomes]
rs7601416	1.00[EUR][1000 genomes]
rs7602182	1.00[EUR][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	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1005281	chr2:183803173-184093877	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv875485	chr2:183827018-184195265	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1010799	chr2:183855680-184244721	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv536072	chr2:183855680-184244721	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1003519	chr2:183885544-184015868	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183846000-183902000	Weak transcription	Lung	lung
2	chr2:183859600-183899400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:183875400-183899600	Weak transcription	HSMMtube	muscle
4	chr2:183878800-183902000	Weak transcription	Esophagus	oesophagus
5	chr2:183879200-183900200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:183880200-183900800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:183886600-183899600	Weak transcription	NH-A	brain
8	chr2:183886600-183900600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr2:183886800-183900600	Weak transcription	Fetal Stomach	stomach
10	chr2:183887600-183899200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:183887800-183899800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:183888600-183899000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr2:183888800-183899000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:183889800-183899600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:183889800-183900600	Weak transcription	Fetal Lung	lung
16	chr2:183889800-183902000	Weak transcription	Gastric	stomach
17	chr2:183891000-183899200	Weak transcription	NHLF	lung
18	chr2:183891200-183900600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:183891400-183899600	Weak transcription	Fetal Intestine Large	intestine
20	chr2:183891400-183901800	Weak transcription	Small Intestine	intestine
21	chr2:183894000-183900000	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr2:183894000-183900200	Enhancers	Fetal Heart	heart
23	chr2:183894200-183899800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr2:183894600-183899200	Weak transcription	Brain Anterior Caudate	brain
25	chr2:183894600-183902000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:183894600-183902000	Weak transcription	Pancreas	Pancrea
27	chr2:183895000-183900600	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:183895400-183901200	Enhancers	Rectal Smooth Muscle	rectum
29	chr2:183896000-183899200	Enhancers	Stomach Mucosa	stomach
30	chr2:183896200-183899400	Enhancers	NHDF-Ad	bronchial
31	chr2:183896200-183899600	Enhancers	HepG2	liver
32	chr2:183896600-183899400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:183896600-183899400	Enhancers	Hela-S3	cervix
34	chr2:183896600-183900200	Enhancers	NHEK	skin
35	chr2:183896600-183900400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:183896800-183899200	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr2:183896800-183899600	Weak transcription	Fetal Brain Female	brain
38	chr2:183896800-183899800	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr2:183897000-183899600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr2:183897200-183899000	Enhancers	A549	lung
41	chr2:183897200-183899200	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr2:183897200-183899200	Weak transcription	HMEC	breast
43	chr2:183897200-183899400	Weak transcription	Brain Germinal Matrix	brain
44	chr2:183897400-183899200	Active TSS	Aorta	Aorta
45	chr2:183897400-183900200	Weak transcription	Brain Substantia Nigra	brain
46	chr2:183897600-183899000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:183897800-183899000	Enhancers	Brain Angular Gyrus	brain
48	chr2:183897800-183899200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr2:183897800-183899400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:183897800-183899600	Weak transcription	Ovary	ovary

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