Variant report

Variant	rs1457498
Chromosome Location	chr6:70499868-70499869
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	chr6:70499217..70503850-chr6:70504773..70507699,6	K562	blood:

Variant related genes	Relation type
ENSG00000168216	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10498869	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs13437057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16868113	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16868129	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17503698	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs28434733	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3799109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707375	0.97[ASN][1000 genomes]
rs6936974	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9294846	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9294847	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9294849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9446157	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9446159	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9446161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9454865	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9454868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9454873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9454876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9454880	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9454881	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9454887	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9454889	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9454890	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9454892	0.86[CEU][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9454893	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886140	chr6:70354682-70728202	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv830682	chr6:70397851-70592883	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1457498	LMBRD1	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70453800-70505600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr6:70477200-70505200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:70477600-70501600	Weak transcription	Fetal Kidney	kidney
4	chr6:70477600-70505400	Weak transcription	NHDF-Ad	bronchial
5	chr6:70478400-70505000	Weak transcription	Fetal Brain Male	brain
6	chr6:70479600-70500600	Weak transcription	Brain Germinal Matrix	brain
7	chr6:70479800-70506200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:70480200-70506000	Weak transcription	Lung	lung
9	chr6:70481400-70502200	Weak transcription	Spleen	Spleen
10	chr6:70481600-70501000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr6:70481600-70505000	Weak transcription	Aorta	Aorta
12	chr6:70483200-70500800	Weak transcription	Fetal Brain Female	brain
13	chr6:70483400-70501200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:70484200-70505200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:70486400-70501000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:70486400-70501000	Weak transcription	Brain Angular Gyrus	brain
17	chr6:70486400-70501000	Weak transcription	Brain Hippocampus Middle	brain
18	chr6:70486600-70500400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr6:70486600-70501000	Weak transcription	Brain Anterior Caudate	brain
20	chr6:70486600-70501000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr6:70486600-70501200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:70487200-70501800	Weak transcription	Thymus	Thymus
23	chr6:70487200-70505200	Weak transcription	NHLF	lung
24	chr6:70488000-70505200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:70488600-70501200	Weak transcription	Fetal Lung	lung
26	chr6:70490200-70501800	Weak transcription	Esophagus	oesophagus
27	chr6:70490200-70505600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:70490400-70501200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:70490400-70505400	Weak transcription	Fetal Muscle Leg	muscle
30	chr6:70490600-70500200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr6:70490800-70503800	Weak transcription	Dnd41	blood
32	chr6:70490800-70505000	Weak transcription	Hela-S3	cervix
33	chr6:70491000-70500400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:70491000-70500800	Weak transcription	HMEC	breast
35	chr6:70491000-70501000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr6:70491200-70501000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:70491200-70501000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:70491400-70500800	Weak transcription	NHEK	skin
39	chr6:70491600-70504600	Weak transcription	HepG2	liver
40	chr6:70492800-70500600	Weak transcription	Colon Smooth Muscle	Colon
41	chr6:70492800-70505000	Weak transcription	Primary T cells from cord blood	blood
42	chr6:70494000-70505400	Weak transcription	Fetal Stomach	stomach
43	chr6:70495200-70501000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr6:70495200-70504000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr6:70495400-70500400	Weak transcription	Fetal Heart	heart
46	chr6:70495400-70501400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr6:70495400-70506000	Weak transcription	Stomach Mucosa	stomach
48	chr6:70495600-70500800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr6:70495600-70500800	Weak transcription	Small Intestine	intestine
50	chr6:70495600-70501200	Weak transcription	Stomach Smooth Muscle	stomach

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