Variant report

Variant	rs175922
Chromosome Location	chr17:19825579-19825580
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11204419	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204420	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204421	0.82[ASN][1000 genomes]
rs119672	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1479129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1638525	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs166840	0.85[EUR][1000 genomes]
rs169412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs169414	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs175921	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1860302	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs191865	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs203450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203451	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203452	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203455	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs203456	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203459	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs203460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203461	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203462	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203465	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203469	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203470	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203479	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203482	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2108978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35003563	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs397969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs427798	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4924803	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs4925060	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4925065	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs4925072	0.88[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs4925077	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs4925081	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs56153261	0.86[ASN][1000 genomes]
rs6587206	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7207625	0.87[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs7208025	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs7208365	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs7209734	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs7222403	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8066150	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs850623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888423	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs918227	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs9899357	0.84[CEU][hapmap];0.80[GIH][hapmap];0.90[TSI][hapmap]
rs9907752	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9914273	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9914304	0.89[EUR][1000 genomes]
rs9916675	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs175922	TMEM11	cis	cerebellum	SCAN
rs175922	AKAP10	cis	lesional skin	skin_eQTL
rs175922	CYTSB	cis	cerebellum	SCAN
rs175922	AKAP10	cis	uninvolved skin	skin_eQTL
rs175922	SPECC1	Cis_1M	lymphoblastoid	RTeQTL
rs175922	AKAP10	cis	lymphoblastoid	seeQTL
rs175922	AKAP10	cis	normal skin	skin_eQTL
rs175922	SNORD49B	cis	parietal	SCAN
rs175922	AKAP10	cis	Lymphoblastoid	GTEx
rs175922	ALDH3A1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19802800-19829000	Strong transcription	Fetal Muscle Leg	muscle
2	chr17:19802800-19844400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr17:19802800-19846400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr17:19802800-19852400	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr17:19803000-19851800	Strong transcription	Fetal Thymus	thymus
6	chr17:19803200-19840800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr17:19803600-19826200	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr17:19803600-19829800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:19803600-19845400	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr17:19803600-19848000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr17:19803800-19830800	Strong transcription	Primary B cells from peripheral blood	blood
12	chr17:19804000-19844400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr17:19804000-19853000	Strong transcription	Dnd41	blood
14	chr17:19806200-19844000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr17:19806200-19844600	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr17:19806400-19830200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr17:19806400-19846200	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr17:19807000-19825800	Strong transcription	Placenta	Placenta
19	chr17:19807800-19843800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr17:19808200-19828400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr17:19809200-19832200	Weak transcription	Fetal Brain Male	brain
22	chr17:19809400-19837400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr17:19809800-19828000	Weak transcription	K562	blood
24	chr17:19810000-19830800	Strong transcription	Adipose Nuclei	Adipose
25	chr17:19810200-19826200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr17:19810200-19826400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr17:19810200-19836600	Weak transcription	Fetal Heart	heart
28	chr17:19811800-19834800	Weak transcription	Small Intestine	intestine
29	chr17:19812200-19845400	Strong transcription	Liver	Liver
30	chr17:19813200-19827200	Weak transcription	Colonic Mucosa	Colon
31	chr17:19813200-19828000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr17:19813200-19833800	Weak transcription	Pancreas	Pancrea
33	chr17:19814200-19828600	Strong transcription	Fetal Stomach	stomach
34	chr17:19814400-19828400	Strong transcription	Fetal Intestine Small	intestine
35	chr17:19815000-19838600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr17:19815200-19828400	Strong transcription	Fetal Intestine Large	intestine
37	chr17:19816600-19826000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr17:19816800-19844400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr17:19817200-19825600	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr17:19817800-19844200	Weak transcription	Stomach Mucosa	stomach
41	chr17:19818200-19830600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr17:19818200-19836400	Strong transcription	A549	lung
43	chr17:19818600-19839400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr17:19819000-19825800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr17:19819600-19826000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr17:19819600-19826000	Weak transcription	Ovary	ovary
47	chr17:19819600-19833600	Weak transcription	Brain Substantia Nigra	brain
48	chr17:19819600-19844600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr17:19819800-19833800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr17:19820000-19832200	Weak transcription	Brain Cingulate Gyrus	brain

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