Variant report

Variant	rs7820738
Chromosome Location	chr8:8702607-8702608
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:8690681..8693173-chr8:8702089..8703698,2	K562	blood:
2	chr8:8702216..8704089-chr8:8704217..8706450,3	K562	blood:
3	chr8:8700876..8702998-chr8:8749130..8751799,2	MCF-7	breast:
4	chr8:8701145..8703921-chr8:8717164..8719093,2	K562	blood:

Variant related genes	Relation type
ENSG00000147324	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1039917	0.82[CEU][hapmap]
rs11249896	0.81[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs13259070	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1510934	0.85[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1533058	0.94[CHB][hapmap];0.80[TSI][hapmap]
rs1533059	0.94[CHB][hapmap];0.82[TSI][hapmap]
rs1877119	0.89[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1964719	0.86[ASN][1000 genomes]
rs2409096	0.89[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3925830	0.82[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs3958877	0.83[ASN][1000 genomes]
rs4841054	0.94[CHB][hapmap];0.92[ASN][1000 genomes]
rs7013471	0.81[CEU][hapmap]
rs7820146	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7833171	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs907180	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs907181	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[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	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7820738	CTSB	cis	cerebellum	SCAN
rs7820738	C8orf13	cis	multi-tissue	Pritchard
rs7820738	FLJ10661	cis	cerebellum	SCAN
rs7820738	PRSS55	cis	cerebellum	SCAN
rs7820738	DKFZp761P0423	cis	multi-tissue	Pritchard
rs7820738	MFHAS1	cis	cerebellum	SCAN
rs7820738	FAM86B3P	cis	Esophagus Mucosa	GTEx
rs7820738	PPP1R3B	cis	cerebellum	SCAN
rs7820738	SGK223	cis	Thyroid	GTEx
rs7820738	CLDN23	cis	multi-tissue	Pritchard

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8670400-8705400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr8:8684600-8703800	Weak transcription	Dnd41	blood
3	chr8:8686600-8705600	Weak transcription	Right Atrium	heart
4	chr8:8687600-8706600	Weak transcription	Lung	lung
5	chr8:8692200-8717600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr8:8692600-8703200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr8:8692600-8707000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr8:8697200-8704000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr8:8699000-8705600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr8:8699200-8703800	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr8:8699400-8705400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr8:8699400-8729600	Weak transcription	Fetal Stomach	stomach
13	chr8:8699800-8704000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr8:8699800-8705800	Enhancers	Primary T cells fromperipheralblood	blood
15	chr8:8700000-8705600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr8:8700000-8707400	Enhancers	Fetal Thymus	thymus
17	chr8:8700200-8705400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr8:8700200-8705400	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr8:8700200-8706200	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr8:8700200-8707400	Enhancers	Fetal Kidney	kidney
21	chr8:8700200-8708000	Weak transcription	Spleen	Spleen
22	chr8:8700400-8704000	Weak transcription	Fetal Brain Female	brain
23	chr8:8700400-8706800	Weak transcription	Esophagus	oesophagus
24	chr8:8700800-8705000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr8:8700800-8705600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr8:8701000-8704200	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr8:8701000-8705200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr8:8701000-8705400	Enhancers	GM12878-XiMat	blood
29	chr8:8701000-8705600	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr8:8701000-8705800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr8:8701000-8706600	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr8:8701000-8707800	Enhancers	Fetal Intestine Large	intestine
33	chr8:8701200-8703600	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr8:8701200-8706000	Enhancers	Colon Smooth Muscle	Colon
35	chr8:8701200-8706400	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr8:8701400-8702800	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr8:8701400-8705600	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr8:8701400-8705800	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr8:8701400-8706200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr8:8701400-8708400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr8:8701600-8703000	Enhancers	Hela-S3	cervix
42	chr8:8701600-8703200	Enhancers	Fetal Lung	lung
43	chr8:8701600-8703600	Enhancers	Brain Anterior Caudate	brain
44	chr8:8701600-8704200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr8:8701600-8704800	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr8:8701600-8706000	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr8:8701600-8706000	Enhancers	Fetal Heart	heart
48	chr8:8701600-8706600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr8:8701800-8703400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr8:8701800-8705200	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links