Variant report

Variant	rs9498355
Chromosome Location	chr6:149763410-149763411
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149762143..149764363-chr6:149765543..149768268,2	K562	blood:
2	chr6:149763319..149765484-chr6:149839894..149842239,2	MCF-7	breast:
3	chr6:149763379..149766103-chr6:149776553..149779366,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178199	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1001305	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11155640	0.81[MEX][hapmap]
rs11155642	0.81[MEX][hapmap]
rs11155646	0.91[ASN][1000 genomes]
rs11155654	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192159	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192814	0.91[ASN][1000 genomes]
rs12195922	0.82[ASN][1000 genomes]
rs58747890	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62441727	1.00[ASN][1000 genomes]
rs6911411	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.91[ASN][1000 genomes]
rs6932778	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs7741099	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7747354	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs7747948	1.00[ASN][1000 genomes]
rs7762222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9485385	0.91[ASN][1000 genomes]
rs9485392	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9485394	0.91[ASN][1000 genomes]
rs9485397	1.00[ASN][1000 genomes]
rs9498324	0.81[MEX][hapmap]
rs9498335	0.81[MEX][hapmap]
rs9498349	0.91[ASN][1000 genomes]
rs9498351	0.91[ASN][1000 genomes]
rs9498352	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9498353	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9498354	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9498356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9498358	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997682	0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv470866	chr6:149744632-149806552	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv5533	chr6:149748047-149793072	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv464076	chr6:149755695-149798835	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv604846	chr6:149755695-149798835	ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9498355	RAET1E	cis	cerebellum	SCAN
rs9498355	LRP11	cis	cerebellum	SCAN
rs9498355	LRP11	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149749800-149764400	Weak transcription	Right Atrium	heart
2	chr6:149753400-149770000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr6:149753600-149768400	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr6:149753600-149769600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:149760600-149766600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr6:149760800-149765800	Weak transcription	GM12878-XiMat	blood
7	chr6:149761600-149769600	Weak transcription	Primary B cells from cord blood	blood
8	chr6:149762000-149763600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:149762400-149764600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:149762600-149764400	Weak transcription	Left Ventricle	heart
11	chr6:149762600-149764600	Weak transcription	NH-A	brain
12	chr6:149762600-149770800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:149762800-149771000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr6:149763000-149764400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:149763000-149764400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:149763000-149764800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:149763200-149764200	Weak transcription	Brain Hippocampus Middle	brain
18	chr6:149763200-149764200	Weak transcription	Fetal Lung	lung
19	chr6:149763200-149764200	Weak transcription	Ovary	ovary
20	chr6:149763200-149764400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:149763200-149764600	Weak transcription	Placenta	Placenta
22	chr6:149763200-149765800	Weak transcription	Right Ventricle	heart
23	chr6:149763200-149770000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:149763200-149771000	Weak transcription	Fetal Intestine Small	intestine
25	chr6:149763200-149771400	Weak transcription	Pancreas	Pancrea
26	chr6:149763400-149766000	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links