Variant report

Variant	rs72888459
Chromosome Location	chr2:183877341-183877342
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	chr2:183874817..183877710-chr2:183883545..183886850,4	K562	blood:
2	chr2:183875662..183878487-chr2:183902178..183904297,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000061676	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs17265880	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675089	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35142583	0.84[AFR][1000 genomes]
rs66727515	0.91[EUR][1000 genomes]
rs6711655	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6734848	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6739840	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72886535	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72886536	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72886547	0.84[AFR][1000 genomes]
rs72886597	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72888442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72888444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72888445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72888452	0.92[AFR][1000 genomes]
rs72888453	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72888467	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72888485	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72888487	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7575613	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7595898	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183773400-183877800	Weak transcription	Stomach Mucosa	stomach
2	chr2:183814600-183893600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:183833600-183878400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:183833600-183879600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:183846000-183902000	Weak transcription	Lung	lung
6	chr2:183854000-183898800	Weak transcription	Fetal Brain Male	brain
7	chr2:183859600-183882000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:183859600-183899400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:183862400-183894400	Weak transcription	Placenta	Placenta
10	chr2:183866000-183878000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:183866000-183881400	Weak transcription	HUVEC	blood vessel
12	chr2:183866000-183881800	Weak transcription	Brain Germinal Matrix	brain
13	chr2:183866200-183881400	Weak transcription	Fetal Intestine Large	intestine
14	chr2:183866800-183881400	Weak transcription	Fetal Brain Female	brain
15	chr2:183866800-183881600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:183866800-183885400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:183866800-183889000	Weak transcription	Fetal Lung	lung
18	chr2:183866800-183889200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:183867000-183879000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:183867200-183881400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:183867800-183881800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:183867800-183889200	Weak transcription	Liver	Liver
23	chr2:183868200-183880800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:183873000-183879800	Enhancers	Fetal Heart	heart
25	chr2:183873000-183881400	Weak transcription	Fetal Intestine Small	intestine
26	chr2:183874400-183877400	Enhancers	Muscle Satellite Cultured Cells	--
27	chr2:183874600-183881000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:183874800-183878200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:183875000-183890000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:183875200-183877400	Weak transcription	Psoas Muscle	Psoas
31	chr2:183875200-183877600	Weak transcription	Aorta	Aorta
32	chr2:183875200-183878000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr2:183875200-183878000	Weak transcription	Adipose Nuclei	Adipose
34	chr2:183875200-183878000	Weak transcription	Right Atrium	heart
35	chr2:183875200-183878200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr2:183875200-183878400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:183875200-183878400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:183875200-183878400	Weak transcription	Brain Substantia Nigra	brain
39	chr2:183875200-183878400	Weak transcription	Esophagus	oesophagus
40	chr2:183875200-183878400	Weak transcription	Gastric	stomach
41	chr2:183875200-183878400	Weak transcription	Left Ventricle	heart
42	chr2:183875200-183878400	Weak transcription	Right Ventricle	heart
43	chr2:183875200-183880200	Weak transcription	Small Intestine	intestine
44	chr2:183875200-183881400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:183875200-183882000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:183875200-183882000	Weak transcription	NH-A	brain
47	chr2:183875200-183884800	Weak transcription	Fetal Stomach	stomach
48	chr2:183875200-183885400	Weak transcription	NHDF-Ad	bronchial
49	chr2:183875200-183886000	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:183875200-183888600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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