Variant report

Variant	rs1820506
Chromosome Location	chr15:42207555-42207556
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42182721..42185354-chr15:42206031..42208454,3	K562	blood:
2	chr15:42207550..42209850-chr15:42209914..42212582,2	MCF-7	breast:
3	chr15:42203961..42205680-chr15:42206094..42208991,2	K562	blood:

Variant related genes	Relation type
ENSG00000174171	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1048166	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1048175	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1648810	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1648815	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1648818	0.90[AFR][1000 genomes]
rs1704381	0.83[EUR][1000 genomes]
rs1704386	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1704388	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1704391	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1704396	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6493011	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7183264	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs890502	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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
15	nsv976926	chr15:42202094-42217599	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1820506	SPTBN5	cis	Artery Aorta	GTEx
rs1820506	SPTBN5	cis	Adipose Subcutaneous	GTEx
rs1820506	SPTBN5	cis	Esophagus Muscularis	GTEx
rs1820506	EHD4	Cis_1M	lymphoblastoid	RTeQTL
rs1820506	SPTBN5	cis	lung	GTEx
rs1820506	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	chr15:42187600-42209800	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:42188600-42209600	Strong transcription	NHEK	skin
4	chr15:42189800-42208400	Strong transcription	HUVEC	blood vessel
5	chr15:42190200-42209800	Weak transcription	Hela-S3	cervix
6	chr15:42190400-42218600	Weak transcription	Fetal Lung	lung
7	chr15:42195800-42209000	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:42197200-42209800	Weak transcription	A549	lung
9	chr15:42197200-42210400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr15:42197200-42210800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:42197200-42218600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr15:42197400-42208200	Strong transcription	HSMM	muscle
13	chr15:42197400-42209600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:42197400-42218600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr15:42197800-42208200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:42198200-42212000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr15:42198800-42212000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr15:42199000-42212600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:42199200-42209000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:42199600-42208400	Weak transcription	Fetal Thymus	thymus
21	chr15:42199600-42208400	Strong transcription	GM12878-XiMat	blood
22	chr15:42199800-42207600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:42200200-42209600	Weak transcription	K562	blood
24	chr15:42201200-42225400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:42201800-42210800	Weak transcription	Thymus	Thymus
26	chr15:42201800-42211000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr15:42201800-42211600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:42202000-42208000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr15:42202000-42208200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:42202000-42208400	Weak transcription	Ovary	ovary
31	chr15:42202000-42208600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr15:42202000-42210000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr15:42202200-42207600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:42202200-42208400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr15:42202200-42209600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:42202200-42209600	Weak transcription	Osteobl	bone
37	chr15:42202200-42209800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr15:42202200-42210000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:42202200-42210000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr15:42202200-42210600	Weak transcription	HepG2	liver
41	chr15:42202200-42218400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr15:42202200-42218600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr15:42202200-42225200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr15:42202600-42208400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr15:42202600-42208400	Weak transcription	Liver	Liver
46	chr15:42202800-42209800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:42203200-42207600	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr15:42203200-42208200	Enhancers	Fetal Heart	heart
49	chr15:42203400-42208400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr15:42203400-42209000	Strong transcription	Fetal Intestine Large	intestine

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