Variant report

Variant	rs28534607
Chromosome Location	chr4:15559698-15559699
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15558536..15560795-chr4:15564157..15566350,2	K562	blood:
2	chr4:15555076..15558141-chr4:15558496..15561165,3	K562	blood:

Variant related genes	Relation type
ENSG00000273133	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10003739	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10008875	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10008889	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10012838	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10017295	0.88[EUR][1000 genomes]
rs10020408	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10022610	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10025837	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10026851	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10030313	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10031017	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10034328	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10939621	0.86[ASN][1000 genomes]
rs10939628	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1134634	0.86[ASN][1000 genomes]
rs11932730	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11933521	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11939541	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11942335	0.87[EUR][1000 genomes]
rs11943107	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11945626	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12503015	0.88[EUR][1000 genomes]
rs12508186	0.87[EUR][1000 genomes]
rs12509029	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12511894	0.83[EUR][1000 genomes]
rs12640192	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12644327	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12645849	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12649803	0.87[ASN][1000 genomes]
rs13104845	0.87[ASN][1000 genomes]
rs13116304	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13121363	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1473166	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16892140	0.89[AFR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16892152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041671	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2110361	0.88[ASN][1000 genomes]
rs2160044	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28419165	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28522268	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28528670	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28661857	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3822298	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235380	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4279203	0.82[EUR][1000 genomes]
rs4280723	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4280724	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4393989	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4583752	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4591601	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4642244	0.88[EUR][1000 genomes]
rs4698117	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4698403	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4698405	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4698408	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56041141	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57526178	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59055524	0.88[ASN][1000 genomes]
rs60040560	0.80[EUR][1000 genomes]
rs60813847	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62290565	0.87[ASN][1000 genomes]
rs62290605	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6449146	0.87[ASN][1000 genomes]
rs6449147	0.87[ASN][1000 genomes]
rs6449149	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6831286	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6839438	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73125606	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73125616	0.87[EUR][1000 genomes]
rs73125627	0.87[EUR][1000 genomes]
rs73125637	0.87[EUR][1000 genomes]
rs73127647	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7377825	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs741180	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs759212	0.87[ASN][1000 genomes]
rs7661102	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7665390	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7665915	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7682586	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7687010	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7692607	0.81[ASN][1000 genomes]
rs7697314	0.87[ASN][1000 genomes]
rs872678	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9996452	0.88[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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers 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 target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15487400-15570400	Weak transcription	Psoas Muscle	Psoas
2	chr4:15502800-15577600	Weak transcription	Right Ventricle	heart
3	chr4:15509200-15564400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:15512000-15580000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:15513000-15562400	Weak transcription	Primary B cells from cord blood	blood
6	chr4:15517800-15593600	Weak transcription	HUVEC	blood vessel
7	chr4:15520000-15572400	Weak transcription	Small Intestine	intestine
8	chr4:15537200-15565000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr4:15537400-15621000	Weak transcription	Hela-S3	cervix
10	chr4:15539000-15570400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr4:15540200-15561600	Weak transcription	HMEC	breast
12	chr4:15540200-15561600	Weak transcription	NHEK	skin
13	chr4:15540200-15562600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:15540400-15563200	Weak transcription	Brain Substantia Nigra	brain
15	chr4:15540400-15565000	Weak transcription	NHDF-Ad	bronchial
16	chr4:15543800-15570600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr4:15544400-15562400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr4:15544600-15563600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:15544800-15571600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr4:15544800-15576200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr4:15545000-15575600	Weak transcription	Fetal Heart	heart
22	chr4:15546000-15589600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:15546200-15564400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:15546200-15569400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr4:15546400-15572600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr4:15546800-15569200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:15548800-15570800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:15549400-15565600	Weak transcription	Primary T cells from cord blood	blood
29	chr4:15549600-15564400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr4:15549600-15570800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:15550000-15617800	Weak transcription	Thymus	Thymus
32	chr4:15554000-15563600	Strong transcription	Stomach Smooth Muscle	stomach
33	chr4:15554000-15572800	Strong transcription	Fetal Brain Female	brain
34	chr4:15554200-15560400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:15554200-15560400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:15554200-15560400	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:15554400-15559800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr4:15554400-15559800	Weak transcription	HepG2	liver
39	chr4:15554400-15560400	Strong transcription	Aorta	Aorta
40	chr4:15554400-15560600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:15554600-15560200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:15554600-15560400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr4:15554600-15560400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr4:15554600-15560400	Strong transcription	Ovary	ovary
45	chr4:15554600-15560600	Strong transcription	Fetal Muscle Leg	muscle
46	chr4:15554600-15560800	Strong transcription	Adipose Nuclei	Adipose
47	chr4:15554600-15601400	Weak transcription	A549	lung
48	chr4:15554800-15561400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:15555000-15562400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr4:15555000-15566800	Weak transcription	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links