Variant report

Variant	rs28709375
Chromosome Location	chr1:222822999-222823000
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222817285..222820043-chr1:222820783..222823555,3	K562	blood:
2	chr1:222816842..222820047-chr1:222820781..222823646,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BROX-3	chr1:222822605-222823133	NONHSAT009692

Variant related genes	Relation type
ENSG00000154305	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10495198	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1133220	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12138316	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17011666	0.85[ASN][1000 genomes]
rs17011681	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17163301	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17163313	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17163345	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17163358	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17163360	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17163363	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17465637	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17465940	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17465982	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1909195	0.85[ASN][1000 genomes]
rs1909197	0.94[ASN][1000 genomes]
rs2133187	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2133189	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2270707	0.93[ASN][1000 genomes]
rs2291832	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2291834	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2378584	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34032254	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34767248	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35158675	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35175385	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35626308	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35700460	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35725247	0.80[ASN][1000 genomes]
rs3748626	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4575092	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4846384	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4846769	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4846770	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61824331	0.80[ASN][1000 genomes]
rs67180937	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71524942	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222818200-222823000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:222818200-222826000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:222818200-222826000	Weak transcription	Ovary	ovary
4	chr1:222818200-222826000	Weak transcription	Spleen	Spleen
5	chr1:222818200-222826200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:222818200-222826200	Weak transcription	Esophagus	oesophagus
7	chr1:222818400-222823000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr1:222818400-222823000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:222818400-222823000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:222818400-222823200	Weak transcription	Brain Germinal Matrix	brain
11	chr1:222818400-222824000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:222818400-222824800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:222818400-222825600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:222818400-222825600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:222818400-222825600	Weak transcription	Psoas Muscle	Psoas
16	chr1:222818400-222825600	Weak transcription	Small Intestine	intestine
17	chr1:222818400-222826000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:222818400-222826000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:222818400-222826000	Weak transcription	Gastric	stomach
20	chr1:222818400-222826000	Weak transcription	Pancreas	Pancrea
21	chr1:222818400-222826000	Weak transcription	Right Ventricle	heart
22	chr1:222818400-222826200	Weak transcription	Aorta	Aorta
23	chr1:222818400-222826600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:222818400-222827600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:222818400-222833600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:222818800-222823000	Weak transcription	Fetal Brain Male	brain
27	chr1:222818800-222823000	Weak transcription	HSMMtube	muscle
28	chr1:222818800-222823200	Weak transcription	Brain Angular Gyrus	brain
29	chr1:222818800-222823200	Weak transcription	Brain Anterior Caudate	brain
30	chr1:222818800-222823200	Weak transcription	Brain Substantia Nigra	brain
31	chr1:222818800-222823800	Weak transcription	HMEC	breast
32	chr1:222818800-222826000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:222818800-222826000	Weak transcription	Fetal Heart	heart
34	chr1:222818800-222841600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:222819000-222823000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:222819000-222823000	Weak transcription	NHEK	skin
37	chr1:222819000-222823200	Weak transcription	K562	blood
38	chr1:222819000-222824000	Weak transcription	A549	lung
39	chr1:222819000-222824800	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:222819000-222825200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:222819000-222825400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:222819000-222825600	Weak transcription	Stomach Mucosa	stomach
43	chr1:222819000-222825800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr1:222819000-222841800	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:222819200-222823000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:222819200-222823000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:222819200-222823000	Weak transcription	GM12878-XiMat	blood
48	chr1:222819200-222823200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:222819200-222823200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:222819200-222825600	Weak transcription	Hela-S3	cervix

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