Variant report

Variant	rs4925060
Chromosome Location	chr17:19863258-19863259
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19861980..19864455-chr17:19872126..19874970,2	K562	blood:
2	chr17:19861091..19865827-chr17:19879221..19882528,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108599	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11204419	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204420	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204421	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11868116	0.83[YRI][hapmap]
rs119672	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1479129	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]
rs1638525	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs166840	0.81[EUR][1000 genomes]
rs169412	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs169414	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs175921	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs175922	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]
rs1860302	0.87[CHB][hapmap]
rs191865	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2013443	0.83[YRI][hapmap]
rs203450	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203451	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203452	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203455	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs203456	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203457	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203458	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203459	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs203460	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203461	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203462	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203465	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203466	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203469	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs203470	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203477	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203479	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203481	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203482	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2108978	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35003563	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs397969	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs427798	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4479308	0.84[ASN][1000 genomes]
rs4924803	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs4925065	0.87[CHB][hapmap]
rs4925072	0.82[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap]
rs4925077	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs4925081	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs56153261	0.84[ASN][1000 genomes]
rs6587206	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207625	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs7208025	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs7208365	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs7209734	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs7222403	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066150	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8078716	0.80[YRI][hapmap]
rs850623	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs860335	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs888423	0.87[CHB][hapmap]
rs918227	0.81[CHB][hapmap]
rs9899357	0.84[CEU][hapmap]
rs9907752	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9914273	1.00[CEU][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9914304	0.85[EUR][1000 genomes]
rs9916675	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4925060	AKAP10	cis	normal skin	skin_eQTL
rs4925060	AKAP10	cis	lesional skin	skin_eQTL
rs4925060	AKAP10	cis	uninvolved skin	skin_eQTL
rs4925060	AKAP10	cis	multi-tissue	Pritchard
rs4925060	SPECC1	Cis_1M	lymphoblastoid	RTeQTL
rs4925060	AKAP10	cis	Lymphoblastoid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19840000-19879200	Weak transcription	Fetal Brain Male	brain
2	chr17:19846800-19875600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr17:19850600-19879200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr17:19850600-19880200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr17:19850600-19880200	Weak transcription	Aorta	Aorta
6	chr17:19851600-19871600	Weak transcription	Colonic Mucosa	Colon
7	chr17:19852000-19871000	Weak transcription	Small Intestine	intestine
8	chr17:19852200-19865000	Weak transcription	Ovary	ovary
9	chr17:19852200-19866000	Weak transcription	Spleen	Spleen
10	chr17:19852200-19879400	Weak transcription	Esophagus	oesophagus
11	chr17:19852200-19879600	Weak transcription	Right Ventricle	heart
12	chr17:19852200-19880000	Weak transcription	Psoas Muscle	Psoas
13	chr17:19852800-19869800	Weak transcription	Fetal Heart	heart
14	chr17:19854400-19864000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr17:19857000-19868800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr17:19857200-19866400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr17:19857200-19867000	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr17:19857200-19875000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr17:19857400-19873800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr17:19857400-19880400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr17:19857600-19866600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr17:19857600-19874000	Strong transcription	Dnd41	blood
23	chr17:19857600-19874400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr17:19857600-19875200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr17:19857600-19880200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr17:19857800-19866600	Strong transcription	Fetal Intestine Large	intestine
27	chr17:19858000-19866400	Strong transcription	Fetal Stomach	stomach
28	chr17:19858200-19867200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr17:19858400-19865600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr17:19858400-19873600	Strong transcription	Duodenum Mucosa	Duodenum
31	chr17:19858600-19865800	Strong transcription	Adipose Nuclei	Adipose
32	chr17:19858600-19874400	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr17:19858600-19875800	Strong transcription	Primary B cells from cord blood	blood
34	chr17:19859000-19877200	Strong transcription	Fetal Thymus	thymus
35	chr17:19859200-19866600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr17:19859200-19870800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr17:19859200-19874400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr17:19859200-19875600	Strong transcription	Placenta	Placenta
39	chr17:19859200-19878600	Strong transcription	Primary B cells from peripheral blood	blood
40	chr17:19859600-19866000	Strong transcription	Fetal Lung	lung
41	chr17:19859600-19876800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr17:19859800-19866400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr17:19859800-19866600	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr17:19859800-19879400	Weak transcription	Brain Angular Gyrus	brain
45	chr17:19860200-19866600	Strong transcription	Liver	Liver
46	chr17:19860800-19863800	Weak transcription	Fetal Intestine Small	intestine
47	chr17:19860800-19864200	Weak transcription	Lung	lung
48	chr17:19861000-19863600	Strong transcription	Primary hematopoietic stem cells	blood
49	chr17:19861000-19866400	Strong transcription	Thymus	Thymus
50	chr17:19861000-19875600	Strong transcription	Rectal Mucosa Donor 29	rectum

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