Variant report

Variant	rs4559208
Chromosome Location	chr8:11153925-11153926
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:11146765..11148444-chr8:11152337..11154487,2	K562	blood:
2	chr8:11142870..11145744-chr8:11152405..11154351,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10098488	0.81[AMR][1000 genomes]
rs10099569	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10104728	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10107010	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11250127	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11775635	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13270679	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13279067	0.86[EUR][1000 genomes]
rs1435278	0.82[EUR][1000 genomes]
rs17797443	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1897950	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1897951	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2060465	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2099456	0.85[EUR][1000 genomes]
rs2164272	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2164273	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2293855	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2293856	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2572419	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28507159	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35392635	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3808509	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3808513	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3808518	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3808519	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4568582	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4840554	0.85[EUR][1000 genomes]
rs6601578	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6601579	0.86[EUR][1000 genomes]
rs6984759	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6985146	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6985460	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6991074	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6991606	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7003241	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7004362	0.88[EUR][1000 genomes]
rs718427	0.86[EUR][1000 genomes]
rs765731	0.81[EUR][1000 genomes]
rs7837036	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][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	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv831233	chr8:11046854-11234384	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1022525	chr8:11066191-11309356	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv539474	chr8:11066191-11309356	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1033312	chr8:11126800-11252170	Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4559208	THEX1	Cis_chr	lymphoblastoid	RTeQTL
rs4559208	MTMR9	Cis_1M	lymphoblastoid	RTeQTL
rs4559208	C8orf5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11143000-11162200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:11143000-11166400	Weak transcription	Esophagus	oesophagus
3	chr8:11143000-11166400	Weak transcription	Pancreas	Pancrea
4	chr8:11143400-11154000	Weak transcription	Psoas Muscle	Psoas
5	chr8:11143400-11163600	Weak transcription	Brain Angular Gyrus	brain
6	chr8:11143400-11166400	Weak transcription	HSMMtube	muscle
7	chr8:11143800-11169000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr8:11144000-11163200	Weak transcription	Right Ventricle	heart
9	chr8:11144400-11156000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr8:11144600-11165200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr8:11145000-11154000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr8:11145000-11157400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr8:11145200-11155000	Weak transcription	Ovary	ovary
14	chr8:11146400-11162400	Weak transcription	Lung	lung
15	chr8:11146600-11155200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr8:11146600-11162400	Weak transcription	Gastric	stomach
17	chr8:11146600-11163600	Weak transcription	Fetal Intestine Small	intestine
18	chr8:11146800-11162400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr8:11146800-11166200	Weak transcription	Spleen	Spleen
20	chr8:11147000-11155000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr8:11147000-11155000	Weak transcription	Fetal Stomach	stomach
22	chr8:11147600-11155200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr8:11147600-11162400	Weak transcription	Brain Substantia Nigra	brain
24	chr8:11147600-11165800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr8:11147600-11166400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr8:11149800-11162200	Weak transcription	Stomach Mucosa	stomach
27	chr8:11150000-11154000	Weak transcription	Colon Smooth Muscle	Colon
28	chr8:11150000-11159400	Weak transcription	Aorta	Aorta
29	chr8:11150200-11162400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr8:11150400-11155200	Weak transcription	Hela-S3	cervix
31	chr8:11150800-11157200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr8:11150800-11169800	Weak transcription	Small Intestine	intestine
33	chr8:11151800-11156800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr8:11152000-11168200	Weak transcription	Fetal Heart	heart
35	chr8:11152000-11169800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr8:11152200-11154800	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr8:11152400-11161800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr8:11152600-11154000	Strong transcription	Fetal Brain Male	brain
39	chr8:11152600-11154200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
40	chr8:11152600-11154400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr8:11152600-11154600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr8:11152600-11154600	Strong transcription	Placenta	Placenta
43	chr8:11152600-11155000	ZNF genes & repeats	Dnd41	blood
44	chr8:11152600-11155200	ZNF genes & repeats	A549	lung
45	chr8:11152600-11159600	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr8:11152800-11154000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr8:11152800-11154200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
48	chr8:11152800-11154200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
49	chr8:11152800-11154200	ZNF genes & repeats	Primary T cells from cord blood	blood
50	chr8:11152800-11154200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links