Variant report

Variant	rs28587961
Chromosome Location	chr1:228367200-228367201
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228361831..228364310-chr1:228365605..228367870,2	MCF-7	breast:
2	chr1:228291103..228294046-chr1:228365844..228368081,3	K562	blood:
3	chr1:228352925..228354845-chr1:228364134..228367346,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181873	Chromatin interaction
ENSG00000143793	Chromatin interaction
ENSG00000203684	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10127705	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10495278	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10495279	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10916266	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1094602	1.00[EUR][1000 genomes]
rs1094603	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11577976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11580599	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11581169	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11582369	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12034268	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12039801	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1771486	0.85[EUR][1000 genomes]
rs1803695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34687764	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3795773	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3795774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41303083	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4653906	0.90[EUR][1000 genomes]
rs4653908	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4653909	0.90[EUR][1000 genomes]
rs4653914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61825156	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61825157	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61825159	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61827462	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6663726	0.90[EUR][1000 genomes]
rs6668719	0.90[EUR][1000 genomes]
rs7530253	1.00[EUR][1000 genomes]
rs7537552	0.90[EUR][1000 genomes]
rs9287011	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9970544	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
8	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
9	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
10	nsv549289	chr1:228327999-228371098	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
11	nsv873260	chr1:228334277-228371098	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
12	nsv873262	chr1:228340653-228371098	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
13	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
14	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
15	esv1808523	chr1:228359177-228400358	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228354400-228384600	Weak transcription	Aorta	Aorta
2	chr1:228354600-228370400	Weak transcription	Right Atrium	heart
3	chr1:228354600-228382200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:228354600-228385200	Weak transcription	Left Ventricle	heart
5	chr1:228354800-228370800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:228354800-228371200	Weak transcription	HSMMtube	muscle
7	chr1:228354800-228373200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:228355000-228370600	Weak transcription	HepG2	liver
9	chr1:228355000-228372400	Weak transcription	Stomach Mucosa	stomach
10	chr1:228355000-228373200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:228355000-228373200	Weak transcription	Hela-S3	cervix
12	chr1:228362600-228368600	Weak transcription	Psoas Muscle	Psoas
13	chr1:228363200-228367200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:228363200-228368200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:228363200-228373200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:228363200-228373200	Weak transcription	Fetal Thymus	thymus
17	chr1:228363400-228367200	Weak transcription	NHLF	lung
18	chr1:228363400-228367400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:228363400-228375000	Weak transcription	Esophagus	oesophagus
20	chr1:228363400-228375800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:228363400-228386400	Weak transcription	Brain Angular Gyrus	brain
22	chr1:228363600-228368000	Weak transcription	NHEK	skin
23	chr1:228363600-228373200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:228363600-228374800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr1:228363800-228368800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:228363800-228373400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:228363800-228385200	Weak transcription	Adipose Nuclei	Adipose
28	chr1:228364000-228369200	Weak transcription	Colonic Mucosa	Colon
29	chr1:228364000-228371600	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:228364000-228373000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:228364000-228373000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:228364000-228373200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:228364000-228384800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:228364200-228371800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:228364400-228368800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:228364400-228386600	Weak transcription	Brain Hippocampus Middle	brain
37	chr1:228364400-228388600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:228364600-228369000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:228364600-228373000	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:228364600-228386600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:228364800-228368400	Enhancers	Primary hematopoietic stem cells	blood
42	chr1:228364800-228370800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:228364800-228373400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:228364800-228375800	Weak transcription	Brain Germinal Matrix	brain
45	chr1:228364800-228385600	Weak transcription	Brain Anterior Caudate	brain
46	chr1:228365000-228367400	Weak transcription	Pancreas	Pancrea
47	chr1:228365000-228371600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:228365000-228373000	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr1:228365000-228377600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:228365000-228379600	Weak transcription	Gastric	stomach

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