Variant report

Variant	rs10028111
Chromosome Location	chr4:88259978-88259979
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	chr4:88256379..88257982-chr4:88259770..88261744,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10003964	0.90[EUR][1000 genomes]
rs10004027	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10012256	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10028441	0.89[ASN][1000 genomes]
rs10050247	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11732896	0.88[ASN][1000 genomes]
rs12649727	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13118664	0.91[ASN][1000 genomes]
rs13119654	0.91[ASN][1000 genomes]
rs28433555	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28445336	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28514476	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28599772	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28636836	0.80[ASN][1000 genomes]
rs28830804	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57041248	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57154655	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58073039	0.89[ASN][1000 genomes]
rs59107493	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6531981	0.89[ASN][1000 genomes]
rs66837437	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7685308	0.88[ASN][1000 genomes]
rs7691791	0.89[ASN][1000 genomes]
rs9992651	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats 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	25 gene(s)	inside rSNPs	diseases
2	nsv870296	chr4:88173534-88295927	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv4412	chr4:88237813-88283368	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	18 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	chr4:88253800-88274600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:88254800-88260200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:88254800-88266000	Weak transcription	Brain Angular Gyrus	brain
4	chr4:88254800-88266000	Weak transcription	Fetal Kidney	kidney
5	chr4:88254800-88311800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:88255000-88260200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:88255000-88260600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:88255000-88263000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr4:88255000-88263200	Weak transcription	HSMM	muscle
10	chr4:88255000-88266000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr4:88255000-88268200	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr4:88255000-88292400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:88255200-88267800	Strong transcription	Duodenum Mucosa	Duodenum
14	chr4:88255200-88274400	Weak transcription	GM12878-XiMat	blood
15	chr4:88255200-88285600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:88255200-88293800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:88255400-88261000	Strong transcription	Fetal Lung	lung
18	chr4:88255400-88263200	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr4:88255400-88264600	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr4:88255600-88266200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:88255800-88266200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:88255800-88278200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:88256000-88260000	Weak transcription	K562	blood
24	chr4:88256000-88260200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr4:88256000-88260600	Weak transcription	Psoas Muscle	Psoas
26	chr4:88256000-88260600	Weak transcription	Thymus	Thymus
27	chr4:88256000-88262400	Weak transcription	Lung	lung
28	chr4:88256000-88262400	Weak transcription	Spleen	Spleen
29	chr4:88256000-88263000	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr4:88256000-88263000	Strong transcription	Placenta	Placenta
31	chr4:88256000-88265800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:88256000-88265800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr4:88256000-88266000	Weak transcription	Brain Hippocampus Middle	brain
34	chr4:88256000-88266200	Weak transcription	Aorta	Aorta
35	chr4:88256000-88274800	Weak transcription	A549	lung
36	chr4:88256200-88260000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:88256200-88260600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr4:88256200-88262400	Weak transcription	Pancreas	Pancrea
39	chr4:88256200-88263000	Strong transcription	Liver	Liver
40	chr4:88256200-88265800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr4:88256200-88265800	Weak transcription	Brain Anterior Caudate	brain
42	chr4:88256200-88266000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:88256200-88266800	Weak transcription	NHLF	lung
44	chr4:88256200-88267000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr4:88256200-88267200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr4:88256200-88292800	Weak transcription	Gastric	stomach
47	chr4:88256200-88310600	Weak transcription	Right Ventricle	heart
48	chr4:88256400-88260200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr4:88256400-88262400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:88256400-88263200	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links