Variant report

Variant	rs9899357
Chromosome Location	chr17:19800549-19800550
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	chr17:19769802..19772027-chr17:19799780..19804333,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AKAP10-2	chr17:19800339-19800600	ENSG00000270091.1
2	lnc-AKAP10-2	chr17:19799903-19800583	ENSG00000270091.1

Variant related genes	Relation type
ENSG00000083290	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs119672	0.84[CEU][hapmap];0.80[GIH][hapmap];0.90[TSI][hapmap]
rs1479129	0.84[CEU][hapmap];0.80[GIH][hapmap];0.90[TSI][hapmap]
rs1638525	0.84[CEU][hapmap]
rs166840	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs169412	0.84[CEU][hapmap];0.80[GIH][hapmap];0.90[TSI][hapmap]
rs175922	0.84[CEU][hapmap];0.80[GIH][hapmap];0.90[TSI][hapmap]
rs203450	0.84[CEU][hapmap]
rs203457	0.84[CEU][hapmap];0.80[GIH][hapmap];0.90[TSI][hapmap]
rs203458	0.84[CEU][hapmap];0.80[GIH][hapmap];0.90[TSI][hapmap]
rs203460	0.84[CEU][hapmap]
rs203462	0.84[CEU][hapmap];0.80[GIH][hapmap];0.90[TSI][hapmap]
rs203465	0.84[CEU][hapmap];0.80[GIH][hapmap];0.90[TSI][hapmap]
rs203466	0.84[CEU][hapmap];0.80[GIH][hapmap];0.90[TSI][hapmap]
rs203469	0.81[EUR][1000 genomes]
rs203477	0.84[CEU][hapmap];0.80[GIH][hapmap];0.90[TSI][hapmap]
rs203479	0.84[CEU][hapmap];0.80[GIH][hapmap];0.90[TSI][hapmap]
rs203481	0.84[CEU][hapmap];0.80[GIH][hapmap];0.90[TSI][hapmap]
rs2108978	0.84[CEU][hapmap];0.80[GIH][hapmap];0.90[TSI][hapmap]
rs397969	0.84[CEU][hapmap];0.80[GIH][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs427798	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4925060	0.84[CEU][hapmap]
rs850623	0.84[CEU][hapmap];0.80[GIH][hapmap];0.90[TSI][hapmap]
rs860335	0.84[CEU][hapmap];0.80[GIH][hapmap];0.85[TSI][hapmap]
rs9914273	0.80[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9914304	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv482398	chr17:19673458-19808039	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv518888	chr17:19789453-19804247	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9899357	SNORD49B	cis	parietal	SCAN
rs9899357	AKAP10	cis	normal skin	skin_eQTL
rs9899357	AKAP10	cis	lesional skin	skin_eQTL
rs9899357	AKAP10	cis	lymphoblastoid	seeQTL
rs9899357	TMEM11	cis	cerebellum	SCAN
rs9899357	CYTSB	cis	cerebellum	SCAN
rs9899357	ALDH3A1	cis	parietal	SCAN
rs9899357	AKAP10	cis	uninvolved skin	skin_eQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19794800-19800800	Weak transcription	Spleen	Spleen
2	chr17:19796400-19809800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:19797600-19800600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr17:19798200-19800800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr17:19798400-19804000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr17:19799200-19808400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr17:19799400-19803800	Weak transcription	Thymus	Thymus
8	chr17:19799400-19805000	Weak transcription	Fetal Intestine Large	intestine
9	chr17:19799600-19800600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr17:19799600-19803800	Weak transcription	Primary T cells from cord blood	blood
11	chr17:19799800-19805200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr17:19799800-19806800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr17:19799800-19807000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr17:19800000-19800800	Enhancers	Liver	Liver
15	chr17:19800000-19801600	Enhancers	Fetal Heart	heart
16	chr17:19800000-19802200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr17:19800200-19801600	Enhancers	Colon Smooth Muscle	Colon
18	chr17:19800200-19802000	Enhancers	A549	lung
19	chr17:19800200-19802200	Flanking Active TSS	Hela-S3	cervix
20	chr17:19800200-19802200	Enhancers	HSMMtube	muscle
21	chr17:19800200-19804000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr17:19800400-19800600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr17:19800400-19800600	Enhancers	Brain Angular Gyrus	brain
24	chr17:19800400-19800600	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr17:19800400-19800800	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr17:19800400-19800800	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr17:19800400-19801000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr17:19800400-19801000	Enhancers	Esophagus	oesophagus
29	chr17:19800400-19801000	Enhancers	Left Ventricle	heart
30	chr17:19800400-19801000	Enhancers	Pancreas	Pancrea
31	chr17:19800400-19801200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr17:19800400-19801200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr17:19800400-19801200	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr17:19800400-19801400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr17:19800400-19801400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr17:19800400-19801400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr17:19800400-19801400	Enhancers	Adipose Nuclei	Adipose
38	chr17:19800400-19801400	Enhancers	Duodenum Mucosa	Duodenum
39	chr17:19800400-19801400	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr17:19800400-19801400	Enhancers	Fetal Muscle Leg	muscle
41	chr17:19800400-19801400	Enhancers	Lung	lung
42	chr17:19800400-19801400	Enhancers	Right Atrium	heart
43	chr17:19800400-19801400	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr17:19800400-19801400	Enhancers	Stomach Smooth Muscle	stomach
45	chr17:19800400-19801400	Enhancers	HMEC	breast
46	chr17:19800400-19801400	Enhancers	NHLF	lung
47	chr17:19800400-19801800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr17:19800400-19802000	Enhancers	NHEK	skin
49	chr17:19800400-19802200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr17:19800400-19802200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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