Variant report

Variant	rs1479129
Chromosome Location	chr17:19845769-19845770
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19769581..19771974-chr17:19843282..19846506,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000083290	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11204419	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204420	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204421	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs119672	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1638525	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166840	0.80[EUR][1000 genomes]
rs169412	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs169414	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs175921	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs175922	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]
rs1860302	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs191865	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs203450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203451	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203452	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203455	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs203456	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203457	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203458	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203459	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs203460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203461	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[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];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203466	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203469	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs203470	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203477	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203481	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[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];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203482	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2108978	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs427798	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4479308	0.82[ASN][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];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[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];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8066150	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs850623	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9914273	1.00[CEU][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9914304	0.85[EUR][1000 genomes]
rs9916675	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[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	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
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1479129	AKAP10	cis	Lymphoblastoid	GTEx
rs1479129	TMEM11	cis	cerebellum	SCAN
rs1479129	SPECC1	Cis_1M	lymphoblastoid	RTeQTL
rs1479129	AKAP10	cis	lesional skin	skin_eQTL
rs1479129	AKAP10	cis	lymphoblastoid	seeQTL
rs1479129	ALDH3A1	cis	parietal	SCAN
rs1479129	CYTSB	cis	cerebellum	SCAN
rs1479129	AKAP10	cis	normal skin	skin_eQTL
rs1479129	AKAP10	cis	uninvolved skin	skin_eQTL
rs1479129	SNORD49B	cis	parietal	SCAN
rs1479129	AKAP10	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19802800-19846400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr17:19802800-19852400	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr17:19803000-19851800	Strong transcription	Fetal Thymus	thymus
4	chr17:19803600-19848000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr17:19804000-19853000	Strong transcription	Dnd41	blood
6	chr17:19806400-19846200	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr17:19824800-19845800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr17:19825200-19848400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr17:19825200-19851800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr17:19827600-19851600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr17:19827600-19852800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr17:19830600-19851200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:19831600-19851400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr17:19837800-19846400	Strong transcription	Primary T cells from cord blood	blood
15	chr17:19838600-19851600	Weak transcription	Psoas Muscle	Psoas
16	chr17:19839800-19846000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr17:19839800-19849800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr17:19840000-19846200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr17:19840000-19846600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr17:19840000-19849400	Weak transcription	Colonic Mucosa	Colon
21	chr17:19840000-19851600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr17:19840000-19879200	Weak transcription	Fetal Brain Male	brain
23	chr17:19840200-19848200	Weak transcription	K562	blood
24	chr17:19840400-19846600	Weak transcription	Brain Germinal Matrix	brain
25	chr17:19841200-19848200	Weak transcription	Fetal Brain Female	brain
26	chr17:19841600-19848600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr17:19841600-19852800	Strong transcription	Primary B cells from cord blood	blood
28	chr17:19841800-19851600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr17:19841800-19852600	Strong transcription	Fetal Intestine Large	intestine
30	chr17:19842000-19850000	Weak transcription	Gastric	stomach
31	chr17:19842000-19850000	Weak transcription	Pancreas	Pancrea
32	chr17:19842000-19852600	Strong transcription	Hela-S3	cervix
33	chr17:19842200-19846600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr17:19842400-19846600	Weak transcription	Lung	lung
35	chr17:19842400-19850000	Weak transcription	Aorta	Aorta
36	chr17:19842400-19851800	Strong transcription	Primary hematopoietic stem cells	blood
37	chr17:19842600-19846600	Enhancers	Brain Cingulate Gyrus	brain
38	chr17:19842600-19851600	Strong transcription	GM12878-XiMat	blood
39	chr17:19842800-19846200	Weak transcription	Fetal Intestine Small	intestine
40	chr17:19842800-19846800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr17:19843000-19846800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr17:19843000-19850000	Weak transcription	Right Ventricle	heart
43	chr17:19843200-19846200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr17:19843200-19846200	Weak transcription	Fetal Stomach	stomach
45	chr17:19843200-19846400	Weak transcription	Fetal Muscle Leg	muscle
46	chr17:19843200-19846600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr17:19843200-19846600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr17:19843200-19848600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr17:19843200-19848800	Weak transcription	Esophagus	oesophagus
50	chr17:19843200-19848800	Weak transcription	Spleen	Spleen

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