Variant report

Variant	rs9916675
Chromosome Location	chr17:19900168-19900169
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1034904	0.82[ASN][1000 genomes]
rs11204419	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11204420	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11204421	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11867585	0.83[JPT][hapmap]
rs119672	0.82[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1479129	0.82[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1638525	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs169412	0.82[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs175922	0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs1860302	0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs191865	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs203450	0.88[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs203451	0.81[EUR][1000 genomes]
rs203452	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs203455	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs203456	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs203457	0.82[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs203458	0.82[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs203460	0.88[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs203462	0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs203465	0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap]
rs203466	0.82[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs203470	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs203477	0.82[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs203479	0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs203481	0.82[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs203482	0.81[EUR][1000 genomes]
rs2042046	0.81[CHD][hapmap]
rs2107565	0.81[CHD][hapmap]
rs2108978	0.82[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2108979	0.82[ASN][1000 genomes]
rs2108980	0.85[ASN][1000 genomes]
rs2703800	0.81[CHD][hapmap]
rs35003563	0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap]
rs397969	0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap]
rs4479308	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4924801	0.86[ASN][1000 genomes]
rs4924803	0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap]
rs4925060	0.88[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4925065	0.94[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs4925066	0.86[ASN][1000 genomes]
rs4925067	0.86[ASN][1000 genomes]
rs4925072	0.88[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap]
rs4925077	0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap]
rs4925081	0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap]
rs6587206	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7207625	0.87[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap]
rs7208025	0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap]
rs7208365	0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap]
rs7209734	0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap]
rs7211535	0.85[ASN][1000 genomes]
rs7222403	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8065337	0.82[ASN][1000 genomes]
rs8066150	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs850623	0.82[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs860335	0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs888423	0.94[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap]
rs918227	0.87[CHB][hapmap];0.93[JPT][hapmap]
rs9906625	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9907752	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9909009	0.87[ASN][1000 genomes]
rs9914273	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv3382860	chr17:19894909-19918588	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs9916675	AKAP10	cis	lymphoblastoid	seeQTL
rs9916675	SNORD49B	cis	parietal	SCAN
rs9916675	TMEM11	cis	cerebellum	SCAN
rs9916675	AKAP10	cis	lesional skin	skin_eQTL
rs9916675	AKAP10	cis	uninvolved skin	skin_eQTL
rs9916675	CYTSB	cis	cerebellum	SCAN
rs9916675	SPECC1	Cis_1M	lymphoblastoid	RTeQTL
rs9916675	AKAP10	cis	multi-tissue	Pritchard
rs9916675	AKAP10	cis	Lymphoblastoid	GTEx
rs9916675	AKAP10	cis	normal skin	skin_eQTL
rs9916675	AKAP10	cis	Frontal Cortex	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19896600-19911600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:19899200-19900400	Enhancers	A549	lung
3	chr17:19899400-19900400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr17:19899600-19900400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr17:19899800-19900200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr17:19899800-19900200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:19899800-19900200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:19899800-19900200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr17:19899800-19900200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr17:19899800-19900200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr17:19899800-19900200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr17:19899800-19900200	Enhancers	Esophagus	oesophagus
13	chr17:19899800-19900400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr17:19899800-19900400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr17:19899800-19900400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr17:19899800-19900400	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr17:19899800-19900400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr17:19900000-19900200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr17:19900000-19900200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr17:19900000-19900200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr17:19900000-19900200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
22	chr17:19900000-19900200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr17:19900000-19900200	Enhancers	Brain Anterior Caudate	brain
24	chr17:19900000-19900200	Enhancers	Spleen	Spleen
25	chr17:19900000-19900400	Enhancers	Primary hematopoietic stem cells	blood
26	chr17:19900000-19900400	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr17:19900000-19900400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr17:19900000-19900400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
29	chr17:19900000-19900400	Enhancers	Monocytes-CD14+_RO01746	blood

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