Variant report

Variant	rs28478297
Chromosome Location	chr15:42199365-42199366
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	chr15:42196907..42199684-chr15:42201909..42205293,3	K562	blood:
2	chr15:42188931..42191610-chr15:42197982..42199883,2	K562	blood:

Variant related genes	Relation type
ENSG00000272003	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10518741	0.90[ASN][1000 genomes]
rs11070353	0.82[ASN][1000 genomes]
rs11636923	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11638188	0.83[EUR][1000 genomes]
rs12101334	0.88[EUR][1000 genomes]
rs12708402	0.84[EUR][1000 genomes]
rs12708403	0.83[EUR][1000 genomes]
rs12905012	0.84[EUR][1000 genomes]
rs1704389	0.90[ASN][1000 genomes]
rs17686769	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271283	0.84[EUR][1000 genomes]
rs28396848	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28550631	0.90[ASN][1000 genomes]
rs3088159	0.84[EUR][1000 genomes]
rs67310386	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7172468	0.90[ASN][1000 genomes]
rs8039061	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920696	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv904116	chr15:42076387-42229852	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
5	nsv904118	chr15:42103822-42207905	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
6	nsv904124	chr15:42109975-42207905	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
7	nsv9244	chr15:42110712-42208805	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
8	nsv904125	chr15:42119900-42210393	Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1038933	chr15:42138456-42309087	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
10	nsv904127	chr15:42142912-42207905	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
11	nsv904128	chr15:42147639-42207905	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
12	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
13	nsv904129	chr15:42162957-42207905	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv1054728	chr15:42177772-42310009	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs28478297	SPTBN5	cis	Adipose Subcutaneous	GTEx
rs28478297	SPTBN5	cis	lung	GTEx
rs28478297	SPTBN5	cis	Thyroid	GTEx
rs28478297	SPTBN5	cis	Artery Aorta	GTEx
rs28478297	SPTBN5	cis	Muscle Skeletal	GTEx
rs28478297	SPTBN5	cis	Esophagus Muscularis	GTEx
rs28478297	SPTBN5	cis	Artery Tibial	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42187200-42211800	Weak transcription	Small Intestine	intestine
2	chr15:42187600-42200400	Weak transcription	Stomach Mucosa	stomach
3	chr15:42187600-42200600	Weak transcription	HepG2	liver
4	chr15:42187600-42209800	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:42187800-42206800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:42188600-42209600	Strong transcription	NHEK	skin
7	chr15:42189800-42208400	Strong transcription	HUVEC	blood vessel
8	chr15:42190200-42209800	Weak transcription	Hela-S3	cervix
9	chr15:42190400-42218600	Weak transcription	Fetal Lung	lung
10	chr15:42192600-42204000	Strong transcription	Esophagus	oesophagus
11	chr15:42193400-42200600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:42193600-42200600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr15:42195400-42200600	Weak transcription	NHDF-Ad	bronchial
14	chr15:42195800-42199400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:42195800-42209000	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:42196000-42199400	Genic enhancers	Fetal Muscle Trunk	muscle
17	chr15:42197000-42200600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:42197200-42200400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr15:42197200-42200600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr15:42197200-42200600	Strong transcription	Fetal Intestine Large	intestine
21	chr15:42197200-42200800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr15:42197200-42200800	Weak transcription	Brain Anterior Caudate	brain
23	chr15:42197200-42200800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:42197200-42201000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr15:42197200-42201200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:42197200-42202600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr15:42197200-42204800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:42197200-42209800	Weak transcription	A549	lung
29	chr15:42197200-42210400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr15:42197200-42210800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:42197200-42218600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr15:42197400-42202000	Strong transcription	Placenta Amnion	Placenta Amnion
33	chr15:42197400-42205200	Weak transcription	Brain Angular Gyrus	brain
34	chr15:42197400-42206600	Strong transcription	NHLF	lung
35	chr15:42197400-42206800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:42197400-42208200	Strong transcription	HSMM	muscle
37	chr15:42197400-42209600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:42197400-42218600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr15:42197600-42202200	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:42197600-42202800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:42197600-42202800	Strong transcription	HSMMtube	muscle
42	chr15:42197600-42204000	Weak transcription	Right Atrium	heart
43	chr15:42197600-42206400	Weak transcription	Psoas Muscle	Psoas
44	chr15:42197800-42201000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:42197800-42201200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr15:42197800-42201400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr15:42197800-42202600	Strong transcription	Liver	Liver
48	chr15:42197800-42206800	Strong transcription	Primary T cells from cord blood	blood
49	chr15:42197800-42208200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:42198000-42199400	ZNF genes & repeats	Primary B cells from peripheral blood	blood

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