Variant report

Variant	rs16828564
Chromosome Location	chr2:149097747-149097748
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10206881	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10469577	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11677584	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11683055	0.90[EUR][1000 genomes]
rs12463708	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12466076	0.85[AMR][1000 genomes]
rs12473137	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12474154	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13386157	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13388448	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13390004	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13410839	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13411082	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13427917	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13432173	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16828558	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17355354	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28773905	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4563168	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56178042	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61304079	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6430309	0.82[EUR][1000 genomes]
rs6724259	0.82[EUR][1000 genomes]
rs7590235	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7590487	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009608	chr2:148897348-149133718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv2753542	chr2:149004714-149268503	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1012275	chr2:149031668-149316793	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv523090	chr2:149037012-149110873	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1012123	chr2:149078500-149151358	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv583289	chr2:149091754-149170115	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv875277	chr2:149094415-149178974	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv875278	chr2:149094415-149201775	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:149059400-149100400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:149069400-149100200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr2:149071000-149105000	Weak transcription	Thymus	Thymus
4	chr2:149071400-149100400	Weak transcription	Ovary	ovary
5	chr2:149071800-149100400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:149085400-149100400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:149086400-149099600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:149086400-149099800	Weak transcription	GM12878-XiMat	blood
9	chr2:149086800-149098200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:149086800-149100400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr2:149088400-149100400	Weak transcription	Fetal Kidney	kidney
12	chr2:149089200-149119400	Weak transcription	Fetal Intestine Small	intestine
13	chr2:149089600-149100400	Weak transcription	Fetal Intestine Large	intestine
14	chr2:149089600-149105400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:149090000-149104200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr2:149090400-149100400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:149090400-149100400	Weak transcription	Brain Anterior Caudate	brain
18	chr2:149090600-149100200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:149091000-149100000	Weak transcription	Pancreas	Pancrea
20	chr2:149092400-149100400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr2:149092400-149100400	Weak transcription	Right Ventricle	heart
22	chr2:149092600-149100400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:149092600-149100400	Weak transcription	Adipose Nuclei	Adipose
24	chr2:149092600-149100400	Weak transcription	Brain Angular Gyrus	brain
25	chr2:149092600-149100400	Weak transcription	Fetal Brain Female	brain
26	chr2:149092600-149100400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr2:149092600-149100400	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:149092600-149100400	Weak transcription	Small Intestine	intestine
29	chr2:149092800-149100400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:149092800-149101200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr2:149093000-149100400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:149093000-149100400	Weak transcription	Psoas Muscle	Psoas
33	chr2:149093000-149101200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr2:149093000-149103400	Weak transcription	Aorta	Aorta
35	chr2:149093200-149102400	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:149093200-149104000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr2:149094400-149101600	Weak transcription	Dnd41	blood
38	chr2:149094600-149100400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:149094600-149100400	Weak transcription	Primary B cells from cord blood	blood
40	chr2:149094600-149100400	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:149094600-149100400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:149094600-149100400	Weak transcription	Fetal Lung	lung
43	chr2:149094600-149100400	Weak transcription	Left Ventricle	heart
44	chr2:149094600-149100400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr2:149094600-149100800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr2:149094600-149102400	Weak transcription	Fetal Thymus	thymus
47	chr2:149094600-149115400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:149094600-149119800	Weak transcription	Fetal Stomach	stomach
49	chr2:149094800-149100400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr2:149095000-149103400	Weak transcription	Spleen	Spleen

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