Variant report

Variant	rs28508327
Chromosome Location	chr2:179980396-179980397
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10172589	0.90[ASN][1000 genomes]
rs10173853	1.00[AMR][1000 genomes]
rs10176828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10178559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10186707	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10205588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10207754	1.00[AMR][1000 genomes]
rs10208882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10221811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12328593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12329222	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12611473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12612427	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12613089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12616452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12617364	1.00[AMR][1000 genomes]
rs12622434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13382573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13383806	0.90[ASN][1000 genomes]
rs13391187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13394908	1.00[AMR][1000 genomes]
rs13395559	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13408774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13412820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13417112	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13422693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13429191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16866630	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16866647	0.90[ASN][1000 genomes]
rs28362046	0.90[ASN][1000 genomes]
rs35041512	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6734127	1.00[AMR][1000 genomes]
rs7578417	0.90[ASN][1000 genomes]
rs7581898	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7588135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7601965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7608106	0.90[ASN][1000 genomes]
rs9288024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][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	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS 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	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179967800-179982400	Weak transcription	Fetal Brain Male	brain
2	chr2:179967800-180004400	Weak transcription	Esophagus	oesophagus
3	chr2:179970000-180004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:179970200-179991000	Weak transcription	Psoas Muscle	Psoas
5	chr2:179970800-179985800	Strong transcription	Primary B cells from cord blood	blood
6	chr2:179970800-179987000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr2:179971600-179991400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:179971600-180012600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:179972000-180005200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:179972000-180005200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:179972200-179982400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:179972400-179982200	Strong transcription	Liver	Liver
13	chr2:179972400-179985400	Strong transcription	Stomach Smooth Muscle	stomach
14	chr2:179972400-179986800	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr2:179972400-179987400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr2:179972600-179985200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:179972600-179985200	Weak transcription	Fetal Heart	heart
18	chr2:179972600-180001800	Weak transcription	NHEK	skin
19	chr2:179972800-179989800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:179972800-180014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:179973000-179982400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr2:179973000-179982600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:179973000-179985800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:179973000-179989200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:179973000-180007200	Weak transcription	GM12878-XiMat	blood
26	chr2:179973200-179980800	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr2:179973200-179982200	Weak transcription	Colonic Mucosa	Colon
28	chr2:179973200-179982200	Weak transcription	Stomach Mucosa	stomach
29	chr2:179973200-179986800	Strong transcription	Adipose Nuclei	Adipose
30	chr2:179973200-179987000	Weak transcription	Right Ventricle	heart
31	chr2:179973200-179987400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:179973200-179988400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr2:179973200-179988800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:179973200-179989200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:179973200-179989400	Weak transcription	Primary T cells from cord blood	blood
36	chr2:179973400-179981800	Strong transcription	Osteobl	bone
37	chr2:179973400-179982600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:179973400-179982800	Weak transcription	A549	lung
39	chr2:179973400-179990000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:179973400-180004400	Weak transcription	Pancreas	Pancrea
41	chr2:179973400-180006800	Weak transcription	Small Intestine	intestine
42	chr2:179973400-180012600	Weak transcription	NHLF	lung
43	chr2:179973400-180030200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:179973800-179982000	Strong transcription	Fetal Intestine Large	intestine
45	chr2:179973800-179986800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:179974000-179981800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:179974000-179982400	Strong transcription	NHDF-Ad	bronchial
48	chr2:179974200-179982400	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr2:179974400-179994200	Strong transcription	HepG2	liver
50	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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