Variant report

Variant	rs7299460
Chromosome Location	chr12:48296268-48296269
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48290491..48293041-chr12:48295549..48298546,2	K562	blood:
2	chr12:48293420..48296418-chr12:48372974..48374777,2	K562	blood:
3	chr12:48295052..48296721-chr12:48395942..48397721,2	MCF-7	breast:
4	chr12:48290096..48306593-chr12:48332606..48350271,44	MCF-7	breast:
5	chr12:48244275..48246412-chr12:48294986..48297524,2	MCF-7	breast:
6	chr12:48245078..48247874-chr12:48296202..48297981,2	K562	blood:
7	chr12:48294511..48296971-chr12:48414193..48417151,2	MCF-7	breast:
8	chr12:48276120..48279378-chr12:48295337..48299363,4	MCF-7	breast:
9	chr12:48270125..48272257-chr12:48295028..48297755,2	MCF-7	breast:
10	chr12:48254834..48256905-chr12:48293937..48296372,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000111424	Chromatin interaction
ENSG00000205537	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10083198	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10747527	0.85[CHB][hapmap]
rs10783219	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10783221	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs10875699	0.93[ASN][1000 genomes]
rs11168292	0.91[YRI][hapmap]
rs11168293	0.91[YRI][hapmap]
rs11568820	0.83[JPT][hapmap]
rs12304110	0.90[ASN][1000 genomes]
rs4578458	0.92[ASN][1000 genomes]
rs4578459	0.81[ASN][1000 genomes]
rs4760603	0.93[ASN][1000 genomes]
rs4760655	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4760658	0.91[YRI][hapmap]
rs4760669	0.92[ASN][1000 genomes]
rs4760670	0.81[ASN][1000 genomes]
rs6580644	0.92[ASN][1000 genomes]
rs6580645	0.81[ASN][1000 genomes]
rs7132324	0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7136534	0.82[EUR][1000 genomes]
rs7312286	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7970314	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

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	nsv428589	chr12:48282920-48341192	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7299460	LASS5	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48262000-48296800	Weak transcription	Aorta	Aorta
2	chr12:48286800-48298000	Weak transcription	Right Atrium	heart
3	chr12:48290800-48296400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr12:48290800-48297400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:48291000-48297000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:48291400-48297000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:48293000-48296800	Enhancers	Fetal Intestine Large	intestine
8	chr12:48293000-48297200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr12:48293200-48297000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:48293200-48297400	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr12:48293200-48297400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr12:48293200-48297400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:48293200-48297600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr12:48293400-48296400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:48293400-48296400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:48293400-48297200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr12:48293400-48297400	Enhancers	Esophagus	oesophagus
18	chr12:48293400-48297600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:48293400-48297600	Enhancers	Lung	lung
20	chr12:48293400-48297800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
21	chr12:48293400-48297800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:48293400-48298200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
23	chr12:48293400-48298400	Enhancers	Gastric	stomach
24	chr12:48293400-48298400	Enhancers	Stomach Mucosa	stomach
25	chr12:48293600-48296600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:48293600-48297000	Enhancers	Primary B cells from cord blood	blood
27	chr12:48293600-48297200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr12:48293600-48297400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr12:48293600-48297800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:48293600-48297800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr12:48293800-48296800	Enhancers	Primary hematopoietic stem cells	blood
32	chr12:48293800-48297000	Weak transcription	Small Intestine	intestine
33	chr12:48294000-48297200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr12:48294200-48296400	Enhancers	NHDF-Ad	bronchial
35	chr12:48294200-48296600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr12:48294200-48296800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
37	chr12:48294200-48296800	Enhancers	Hela-S3	cervix
38	chr12:48294200-48298800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr12:48294400-48297000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:48294400-48298200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr12:48294400-48299000	Enhancers	Spleen	Spleen
42	chr12:48294600-48296800	Transcr. at gene 5' and 3'	NHEK	skin
43	chr12:48294600-48297800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr12:48294800-48296800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:48295000-48296800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr12:48295000-48297600	Active TSS	Rectal Smooth Muscle	rectum
47	chr12:48295200-48297200	Enhancers	Fetal Intestine Small	intestine
48	chr12:48295200-48297200	Weak transcription	Pancreas	Pancrea
49	chr12:48295400-48296800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:48295400-48296800	Active TSS	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links