Variant report

Variant	rs408459
Chromosome Location	chr8:8706332-8706333
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:8702216..8704089-chr8:8704217..8706450,3	K562	blood:
2	chr8:8705274..8707873-chr8:8797138..8799236,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1039916	0.91[CHB][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap]
rs11249893	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11249896	0.84[EUR][1000 genomes]
rs11784052	0.89[MEX][hapmap]
rs11995244	0.82[CHB][hapmap]
rs12547493	0.89[MEX][hapmap]
rs12677550	0.82[CHB][hapmap]
rs12682352	0.82[CHB][hapmap];0.89[MEX][hapmap]
rs13254903	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs13259216	0.89[MEX][hapmap]
rs1510932	0.81[CHB][hapmap]
rs1533058	0.89[MEX][hapmap]
rs1533059	0.89[MEX][hapmap]
rs1567398	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs2428	0.82[CHB][hapmap];0.84[MEX][hapmap]
rs332039	0.82[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs332040	0.82[CHB][hapmap];0.80[CHD][hapmap];0.89[MEX][hapmap]
rs3827806	0.82[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap]
rs437895	0.82[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs4382480	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs440788	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4481596	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4523255	0.84[CEU][hapmap]
rs4840362	0.89[MEX][hapmap]
rs4841042	0.89[MEX][hapmap]
rs4841051	0.91[CHB][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap]
rs4841055	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs6601265	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs6996376	0.87[ASN][1000 genomes]
rs907183	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs9329169	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv1019606	chr8:8353661-8736992	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv539456	chr8:8353661-8736992	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	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
5	nsv1022511	chr8:8493992-8737132	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv539457	chr8:8493992-8737132	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv831228	chr8:8608387-8790790	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv1018828	chr8:8609880-8790660	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv1022331	chr8:8610035-8787981	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	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
11	nsv890338	chr8:8669622-8707970	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1015437	chr8:8681255-8723798	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1023221	chr8:8695393-8722418	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv1024055	chr8:8697249-8721016	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv539459	chr8:8697249-8721016	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv3367069	chr8:8706083-8706434	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs408459	MFHAS1	cis	cerebellum	SCAN
rs408459	AC087269.1	cis	Skin Sun Exposed Lower leg	GTEx
rs408459	CLDN23	cis	Skin Sun Exposed Lower leg	GTEx
rs408459	FLJ10661	cis	cerebellum	SCAN
rs408459	C8orf5	Cis_chr	lymphoblastoid	RTeQTL
rs408459	PRSS55	cis	cerebellum	SCAN
rs408459	PPP1R3B	cis	cerebellum	SCAN
rs408459	CTSB	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8687600-8706600	Weak transcription	Lung	lung
2	chr8:8692200-8717600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr8:8692600-8707000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr8:8699400-8729600	Weak transcription	Fetal Stomach	stomach
5	chr8:8700000-8707400	Enhancers	Fetal Thymus	thymus
6	chr8:8700200-8707400	Enhancers	Fetal Kidney	kidney
7	chr8:8700200-8708000	Weak transcription	Spleen	Spleen
8	chr8:8700400-8706800	Weak transcription	Esophagus	oesophagus
9	chr8:8701000-8706600	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr8:8701000-8707800	Enhancers	Fetal Intestine Large	intestine
11	chr8:8701200-8706400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr8:8701400-8708400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr8:8701600-8706600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr8:8701800-8706400	Enhancers	Thymus	Thymus
15	chr8:8702200-8726000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr8:8702200-8726400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr8:8702400-8706800	Weak transcription	Liver	Liver
18	chr8:8702400-8706800	Weak transcription	Pancreas	Pancrea
19	chr8:8702400-8708000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr8:8702400-8708200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr8:8702400-8708200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr8:8702400-8708400	Weak transcription	NH-A	brain
23	chr8:8702400-8709600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr8:8702400-8713600	Weak transcription	Gastric	stomach
25	chr8:8702600-8707000	Enhancers	A549	lung
26	chr8:8703000-8725200	Weak transcription	Hela-S3	cervix
27	chr8:8703200-8709400	Weak transcription	Psoas Muscle	Psoas
28	chr8:8703600-8706800	Weak transcription	Left Ventricle	heart
29	chr8:8703600-8713600	Weak transcription	Brain Substantia Nigra	brain
30	chr8:8704000-8707400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr8:8704200-8709400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr8:8704400-8706800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr8:8704400-8708400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr8:8705000-8706400	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr8:8705000-8706400	Enhancers	Brain Germinal Matrix	brain
36	chr8:8705000-8706800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr8:8705000-8707600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr8:8705000-8708200	Weak transcription	HSMM	muscle
39	chr8:8705000-8723600	Weak transcription	Fetal Muscle Leg	muscle
40	chr8:8705200-8706400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr8:8705200-8707000	Enhancers	HepG2	liver
42	chr8:8705200-8707400	Enhancers	Stomach Smooth Muscle	stomach
43	chr8:8705200-8709600	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr8:8705400-8706400	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr8:8705400-8706400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr8:8705400-8706400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr8:8705400-8706400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr8:8705400-8706400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr8:8705400-8706600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr8:8705400-8706600	Flanking Active TSS	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links