Variant report

Variant	rs6508974
Chromosome Location	chr19:41733145-41733146
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41725446..41729347-chr19:41729788..41733704,5	K562	blood:
2	chr19:41730545..41733193-chr19:41768273..41769945,2	MCF-7	breast:
3	chr19:41732801..41734640-chr19:41767738..41769811,2	K562	blood:
4	chr19:41733057..41734716-chr19:41742855..41744985,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269652	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000167601	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10421990	0.90[CHB][hapmap]
rs11879562	0.90[CHB][hapmap]
rs11882467	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs12327659	0.90[CHB][hapmap]
rs12462203	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12975585	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs12978098	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12978323	0.85[CHB][hapmap]
rs12979764	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12980248	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12980480	0.90[CHB][hapmap]
rs12983047	0.85[CHB][hapmap]
rs12984621	0.98[ASN][1000 genomes]
rs1865051	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs1865053	0.90[CHB][hapmap]
rs2304230	0.90[CHB][hapmap]
rs2304234	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs3745295	0.90[CHB][hapmap]
rs3752705	0.90[CHB][hapmap]
rs3816052	0.90[CHB][hapmap]
rs3826714	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs4456618	0.90[CHB][hapmap]
rs4802111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802112	0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4802113	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4803448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803449	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs67033402	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6957	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs7245398	0.90[CHB][hapmap]
rs7246525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7248164	0.90[CHB][hapmap]
rs7257310	0.85[CHB][hapmap]
rs7258749	0.90[CHB][hapmap]
rs8109167	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs8109627	0.85[CHB][hapmap];0.89[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911768	chr19:41680424-41748753	Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6508974	RTN2	cis	cerebellum	SCAN
rs6508974	ZNF226	cis	cerebellum	SCAN
rs6508974	BAX	cis	cerebellum	SCAN
rs6508974	ZNF155	cis	parietal	SCAN
rs6508974	DKKL1	cis	parietal	SCAN
rs6508974	SIX5	cis	cerebellum	SCAN
rs6508974	ERF	cis	cerebellum	SCAN
rs6508974	FOSB	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41724400-41733200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:41726000-41733200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr19:41730200-41762600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:41731600-41733200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr19:41731600-41733200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:41732200-41733200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:41732400-41733200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:41732400-41733200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr19:41732400-41733200	Flanking Active TSS	Hela-S3	cervix
10	chr19:41732600-41733200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:41732600-41733200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
12	chr19:41732600-41733200	Flanking Active TSS	Fetal Intestine Large	intestine
13	chr19:41732600-41733200	Flanking Active TSS	Fetal Intestine Small	intestine
14	chr19:41732600-41733200	Genic enhancers	Osteobl	bone
15	chr19:41732600-41768800	Weak transcription	Small Intestine	intestine
16	chr19:41732800-41733200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr19:41732800-41733200	Enhancers	H1 Cell Line	embryonic stem cell
18	chr19:41732800-41733200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:41732800-41733200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
20	chr19:41732800-41733200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
21	chr19:41732800-41733200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr19:41732800-41733200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr19:41732800-41733200	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr19:41732800-41733200	Enhancers	Stomach Mucosa	stomach
25	chr19:41732800-41733200	Active TSS	HepG2	liver
26	chr19:41732800-41733200	Genic enhancers	HSMM	muscle
27	chr19:41732800-41733200	Enhancers	HUVEC	blood vessel
28	chr19:41732800-41733200	Genic enhancers	NH-A	brain
29	chr19:41732800-41733200	Genic enhancers	NHEK	skin
30	chr19:41732800-41733400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:41732800-41733400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:41732800-41733400	Enhancers	Fetal Heart	heart
33	chr19:41732800-41733600	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr19:41732800-41734000	Genic enhancers	HMEC	breast
35	chr19:41732800-41734000	Genic enhancers	NHLF	lung
36	chr19:41732800-41734200	Enhancers	Primary hematopoietic stem cells	blood
37	chr19:41732800-41734200	Genic enhancers	HSMMtube	muscle
38	chr19:41732800-41734400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr19:41732800-41734400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:41732800-41735800	Weak transcription	Fetal Lung	lung
41	chr19:41732800-41736200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:41732800-41739200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:41732800-41742800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr19:41732800-41745200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr19:41733000-41733200	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr19:41733000-41733200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
47	chr19:41733000-41733200	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr19:41733000-41733200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr19:41733000-41733200	Enhancers	Primary T cells from cord blood	blood
50	chr19:41733000-41733200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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