Variant report

Variant	rs2228145
Chromosome Location	chr1:154426970-154426971
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11265613	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12126142	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12133641	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12730036	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12730935	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12753254	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4129267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4393147	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4453032	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4537545	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4576655	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845372	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845373	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845620	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845621	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4845622	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845623	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56383622	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61812598	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6664201	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6684439	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7512646	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7518199	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7521458	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7529229	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Rheumatoid arthritis	24390342	GWAS catalog

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154414800-154436000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:154416200-154435800	Strong transcription	Liver	Liver
3	chr1:154417400-154428000	Strong transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:154418000-154428000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:154418000-154440000	Weak transcription	Small Intestine	intestine
6	chr1:154418600-154432800	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr1:154419200-154427200	Weak transcription	Ovary	ovary
8	chr1:154419200-154432200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:154419200-154435800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:154420800-154428000	Strong transcription	Colon Smooth Muscle	Colon
11	chr1:154421800-154431800	Strong transcription	Rectal Smooth Muscle	rectum
12	chr1:154422600-154434400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:154422600-154437600	Weak transcription	Pancreas	Pancrea
14	chr1:154424200-154427000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:154424400-154427800	Genic enhancers	Primary monocytes fromperipheralblood	blood
16	chr1:154424800-154436000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:154425000-154429000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:154425000-154437200	Weak transcription	Fetal Stomach	stomach
19	chr1:154425600-154427000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr1:154425600-154427200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr1:154425600-154428200	Enhancers	Primary B cells from cord blood	blood
22	chr1:154425800-154427000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:154425800-154427000	Enhancers	HMEC	breast
24	chr1:154425800-154427200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr1:154425800-154427200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
26	chr1:154425800-154427200	Enhancers	Fetal Thymus	thymus
27	chr1:154425800-154427200	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
28	chr1:154425800-154427400	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
29	chr1:154426000-154427000	Enhancers	Primary hematopoietic stem cells	blood
30	chr1:154426000-154427800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:154426000-154427800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:154426000-154434200	Weak transcription	Placenta	Placenta
33	chr1:154426000-154436200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:154426200-154427800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:154426200-154427800	Strong transcription	Left Ventricle	heart
36	chr1:154426200-154428600	Strong transcription	Gastric	stomach
37	chr1:154426200-154431000	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:154426200-154433600	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:154426200-154434400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:154426200-154436000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr1:154426400-154427000	Genic enhancers	NHEK	skin
42	chr1:154426400-154427200	Weak transcription	Right Ventricle	heart
43	chr1:154426400-154427800	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr1:154426400-154427800	Strong transcription	Spleen	Spleen
45	chr1:154426400-154427800	Enhancers	GM12878-XiMat	blood
46	chr1:154426400-154428000	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:154426400-154429000	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:154426400-154432000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:154426400-154432800	Strong transcription	Lung	lung
50	chr1:154426400-154434800	Strong transcription	Stomach Smooth Muscle	stomach

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