Variant report

Variant	rs28572014
Chromosome Location	chr8:8793607-8793608
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	chr8:8792434..8796663-chr8:8799601..8802595,4	K562	blood:
2	chr8:8791750..8794485-chr8:8798173..8800628,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ERI1-6	chr8:8793078-8793689	NONHSAT124895

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10091588	1.00[ASN][1000 genomes]
rs10096850	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1036082	1.00[ASN][1000 genomes]
rs11774244	1.00[ASN][1000 genomes]
rs11775788	1.00[ASN][1000 genomes]
rs11779660	1.00[ASN][1000 genomes]
rs11779804	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11780338	1.00[ASN][1000 genomes]
rs11780774	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11781203	1.00[ASN][1000 genomes]
rs13250781	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13277114	1.00[ASN][1000 genomes]
rs1530484	1.00[ASN][1000 genomes]
rs17700611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17701980	1.00[ASN][1000 genomes]
rs2043129	0.81[EUR][1000 genomes]
rs28520356	1.00[ASN][1000 genomes]
rs34293316	1.00[ASN][1000 genomes]
rs36056437	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4840376	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55824072	1.00[ASN][1000 genomes]
rs56349323	1.00[ASN][1000 genomes]
rs56400435	1.00[ASN][1000 genomes]
rs57280925	1.00[ASN][1000 genomes]
rs59041878	1.00[ASN][1000 genomes]
rs59257214	1.00[ASN][1000 genomes]
rs60551984	1.00[ASN][1000 genomes]
rs61397430	1.00[ASN][1000 genomes]
rs61730232	1.00[ASN][1000 genomes]
rs62492947	1.00[ASN][1000 genomes]
rs62493174	1.00[ASN][1000 genomes]
rs62495491	1.00[ASN][1000 genomes]
rs62495539	1.00[ASN][1000 genomes]
rs6981745	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6982619	1.00[ASN][1000 genomes]
rs6987569	1.00[ASN][1000 genomes]
rs6996374	1.00[ASN][1000 genomes]
rs7000323	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7001187	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73518330	1.00[ASN][1000 genomes]
rs73518392	1.00[ASN][1000 genomes]
rs7357482	1.00[ASN][1000 genomes]
rs73662247	1.00[ASN][1000 genomes]
rs7822129	1.00[ASN][1000 genomes]
rs7826478	1.00[ASN][1000 genomes]
rs7828944	1.00[ASN][1000 genomes]
rs7830266	1.00[ASN][1000 genomes]
rs7843024	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7843154	1.00[ASN][1000 genomes]
rs7843369	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7843789	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7846007	1.00[ASN][1000 genomes]
rs895253	1.00[ASN][1000 genomes]
rs9329175	1.00[ASN][1000 genomes]
rs9329176	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv995047	chr8:8353662-8857913	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv831229	chr8:8751523-8926235	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1017388	chr8:8759494-8826714	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1017238	chr8:8760138-8831662	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1026913	chr8:8773659-8838256	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs28572014	RP11-62H7.2	cis	Thyroid	GTEx
rs28572014	C8orf5	Cis_chr	lymphoblastoid	RTeQTL
rs28572014	CTA-398F10.2	cis	Skin Sun Exposed Lower leg	GTEx
rs28572014	THEX1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8779600-8799800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr8:8780600-8799800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr8:8781000-8799800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr8:8781200-8815200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr8:8781600-8816600	Weak transcription	Primary T cells from cord blood	blood
6	chr8:8782400-8799800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr8:8784800-8795800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr8:8786200-8820600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr8:8788200-8796400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr8:8791400-8794000	Enhancers	Placenta	Placenta
11	chr8:8791600-8799600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr8:8792400-8800200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr8:8792600-8793800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr8:8792600-8798600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr8:8792800-8793800	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr8:8792800-8794800	Enhancers	K562	blood
17	chr8:8793000-8793800	Enhancers	Fetal Brain Male	brain
18	chr8:8793000-8794200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr8:8793000-8802600	Weak transcription	Small Intestine	intestine
20	chr8:8793200-8793800	Enhancers	Fetal Brain Female	brain
21	chr8:8793200-8794000	Enhancers	Adipose Nuclei	Adipose
22	chr8:8793200-8795400	Weak transcription	Fetal Thymus	thymus
23	chr8:8793200-8795600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr8:8793200-8796200	Weak transcription	Esophagus	oesophagus
25	chr8:8793200-8796200	Weak transcription	Left Ventricle	heart
26	chr8:8793200-8797000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr8:8793200-8797400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr8:8793400-8795400	Weak transcription	Liver	Liver
29	chr8:8793400-8795600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr8:8793400-8795800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr8:8793400-8796000	Weak transcription	Thymus	Thymus
32	chr8:8793400-8804200	Weak transcription	Right Atrium	heart
33	chr8:8793600-8793800	Bivalent Enhancer	Brain Hippocampus Middle	brain
34	chr8:8793600-8794000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr8:8793600-8794400	Enhancers	Right Ventricle	heart
36	chr8:8793600-8794400	Enhancers	Spleen	Spleen

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