Variant report

Variant	rs28409498
Chromosome Location	chr4:56313285-56313286
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	chr4:56312880..56314520-chr4:56319632..56321569,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11722277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11722415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11723580	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11724300	1.00[AFR][1000 genomes]
rs11725081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11725422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11725439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11725592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11725738	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11727248	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11729092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11729403	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11732078	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11732684	1.00[AFR][1000 genomes]
rs11733959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11733966	1.00[AFR][1000 genomes]
rs11735654	0.95[EUR][1000 genomes]
rs1522113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17085763	0.97[EUR][1000 genomes]
rs28450557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34897046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35133040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35793438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1011722	chr4:56261349-56325600	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56265600-56319800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:56268800-56326000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:56274600-56332200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:56276000-56320000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:56279000-56321800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:56288400-56318400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:56290800-56340400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:56290800-56340600	Weak transcription	Thymus	Thymus
9	chr4:56293000-56324800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:56293000-56354800	Weak transcription	Aorta	Aorta
11	chr4:56294000-56341200	Weak transcription	Small Intestine	intestine
12	chr4:56296200-56314600	Weak transcription	Psoas Muscle	Psoas
13	chr4:56296200-56314600	Weak transcription	Hela-S3	cervix
14	chr4:56301600-56334800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:56301800-56314000	Weak transcription	A549	lung
16	chr4:56301800-56314200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr4:56301800-56316200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:56301800-56316200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:56301800-56318000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:56301800-56318000	Weak transcription	Right Ventricle	heart
21	chr4:56301800-56332200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:56301800-56339200	Weak transcription	Fetal Brain Male	brain
23	chr4:56302000-56314000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr4:56302200-56313400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr4:56302200-56313600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr4:56302200-56314000	Weak transcription	Fetal Heart	heart
27	chr4:56302200-56314400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr4:56302200-56314800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr4:56302200-56315600	Weak transcription	Fetal Stomach	stomach
30	chr4:56302400-56375600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:56303000-56340200	Weak transcription	Colon Smooth Muscle	Colon
32	chr4:56303600-56314200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr4:56304000-56331800	Weak transcription	Esophagus	oesophagus
34	chr4:56304600-56316200	Weak transcription	Lung	lung
35	chr4:56304600-56365600	Weak transcription	Spleen	Spleen
36	chr4:56304800-56314000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr4:56304800-56314600	Weak transcription	Colonic Mucosa	Colon
38	chr4:56304800-56331800	Weak transcription	Gastric	stomach
39	chr4:56304800-56340000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr4:56304800-56375800	Weak transcription	Pancreas	Pancrea
41	chr4:56305000-56314200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr4:56305000-56318200	Weak transcription	HSMMtube	muscle
43	chr4:56305200-56317800	Weak transcription	Brain Germinal Matrix	brain
44	chr4:56305600-56313600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr4:56305800-56314000	Weak transcription	Brain Anterior Caudate	brain
46	chr4:56306000-56313600	Weak transcription	Primary B cells from cord blood	blood
47	chr4:56306000-56314600	Weak transcription	HepG2	liver
48	chr4:56306000-56318200	Weak transcription	Brain Substantia Nigra	brain
49	chr4:56306000-56361200	Weak transcription	Stomach Mucosa	stomach
50	chr4:56306200-56314000	Weak transcription	Brain Angular Gyrus	brain

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