Variant report

Variant	rs55882852
Chromosome Location	chr1:227500559-227500560
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227490028..227493033-chr1:227499168..227502183,4	K562	blood:
2	chr1:227491263..227493925-chr1:227500068..227502093,2	MCF-7	breast:
3	chr1:227500261..227502142-chr1:227623311..227626021,2	K562	blood:
4	chr1:227499595..227501677-chr1:227627472..227629902,2	K562	blood:
5	chr1:227500332..227503244-chr1:227542452..227546426,3	K562	blood:

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1015815	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1015816	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10916109	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10916114	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11801994	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11803590	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11803761	0.91[EUR][1000 genomes]
rs11805298	0.91[EUR][1000 genomes]
rs11806511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11806937	0.91[EUR][1000 genomes]
rs11808928	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11810328	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11811358	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12402456	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12403650	0.93[EUR][1000 genomes]
rs12403986	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12405363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12408913	0.93[EUR][1000 genomes]
rs12410327	0.94[EUR][1000 genomes]
rs12741049	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1464076	0.94[EUR][1000 genomes]
rs1464077	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1513602	0.95[EUR][1000 genomes]
rs1513603	0.91[EUR][1000 genomes]
rs1546557	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1606549	0.94[EUR][1000 genomes]
rs16847492	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16847634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17613166	0.93[EUR][1000 genomes]
rs34125608	0.88[AFR][1000 genomes]
rs34263105	0.94[EUR][1000 genomes]
rs34400564	0.91[EUR][1000 genomes]
rs41270149	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4255349	0.93[EUR][1000 genomes]
rs4282782	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4300186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4354510	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4434814	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4437846	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4518864	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4543764	0.87[EUR][1000 genomes]
rs55805110	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55946024	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57276421	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57758974	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58489467	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59116340	0.91[EUR][1000 genomes]
rs59121440	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59859849	0.95[EUR][1000 genomes]
rs60068245	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60235610	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60742095	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60958272	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61081394	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61522132	0.91[EUR][1000 genomes]
rs6659506	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6668367	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73088658	0.91[EUR][1000 genomes]
rs73090612	0.91[EUR][1000 genomes]
rs73094351	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73094393	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73094400	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73096317	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73096350	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73096353	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73096358	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73096374	0.95[EUR][1000 genomes]
rs73098390	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73098394	0.81[AFR][1000 genomes]
rs73098398	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73100309	0.83[AFR][1000 genomes]
rs73102304	0.81[AFR][1000 genomes]
rs73102307	0.94[EUR][1000 genomes]
rs74140153	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7515739	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7519099	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7526283	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7534286	0.88[EUR][1000 genomes]
rs7535010	0.88[EUR][1000 genomes]
rs7539037	0.91[EUR][1000 genomes]
rs7539750	0.91[EUR][1000 genomes]
rs7542505	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7544923	0.94[EUR][1000 genomes]
rs7545775	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7551556	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227469200-227502600	Weak transcription	HSMM	muscle
2	chr1:227469600-227501800	Weak transcription	Fetal Stomach	stomach
3	chr1:227475000-227502000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:227487000-227501800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:227487000-227501800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:227487000-227502000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:227487600-227502400	Weak transcription	Osteobl	bone
8	chr1:227487800-227501400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:227488000-227501800	Weak transcription	A549	lung
10	chr1:227490200-227503800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:227491400-227501400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:227492600-227503400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:227495000-227503400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:227496200-227502000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:227496200-227504800	Weak transcription	Gastric	stomach
16	chr1:227496400-227501200	Enhancers	HUVEC	blood vessel
17	chr1:227496400-227501800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:227496400-227502000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:227496800-227501800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:227496800-227502000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:227497000-227501600	Weak transcription	NHDF-Ad	bronchial
22	chr1:227497200-227501800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:227497200-227502600	Weak transcription	Fetal Intestine Large	intestine
24	chr1:227497600-227501000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:227497600-227501800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:227497600-227502000	Weak transcription	Liver	Liver
27	chr1:227497800-227501400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:227498000-227501800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:227498200-227501800	Weak transcription	Brain Anterior Caudate	brain
30	chr1:227498200-227501800	Weak transcription	Fetal Lung	lung
31	chr1:227498200-227502000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr1:227498200-227503000	Weak transcription	Brain Germinal Matrix	brain
33	chr1:227498200-227503200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:227498400-227501800	Weak transcription	Adipose Nuclei	Adipose
35	chr1:227498400-227502000	Weak transcription	HepG2	liver
36	chr1:227498800-227501200	Enhancers	Brain Angular Gyrus	brain
37	chr1:227498800-227501800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:227499000-227501200	Enhancers	Brain Hippocampus Middle	brain
39	chr1:227499200-227502400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr1:227499400-227500600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:227499400-227503800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr1:227499600-227500600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:227499600-227500800	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr1:227499600-227502000	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr1:227500000-227502200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:227500200-227500600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr1:227500200-227500600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:227500200-227500600	Enhancers	Muscle Satellite Cultured Cells	--
49	chr1:227500200-227500600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:227500200-227500600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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