Variant report

Variant	rs16959869
Chromosome Location	chr17:16523910-16523911
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16520972..16523245-chr17:16523788..16526094,2	MCF-7	breast:
2	chr17:16515728..16519823-chr17:16521638..16525880,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235554	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1005369	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1005370	1.00[ASN][1000 genomes]
rs12051673	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12103873	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16959857	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16959870	1.00[ASN][1000 genomes]
rs28398264	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28431824	0.98[ASN][1000 genomes]
rs28458310	0.98[ASN][1000 genomes]
rs28458353	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28525101	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28525658	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28526077	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28612609	0.87[ASN][1000 genomes]
rs28626982	0.98[ASN][1000 genomes]
rs28636605	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28674185	0.98[ASN][1000 genomes]
rs28751872	0.98[ASN][1000 genomes]
rs28754336	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28792801	1.00[ASN][1000 genomes]
rs28826699	1.00[ASN][1000 genomes]
rs28865976	1.00[ASN][1000 genomes]
rs28875211	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813762	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4239135	0.83[ASN][1000 genomes]
rs4352086	0.98[ASN][1000 genomes]
rs4791672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4791673	1.00[ASN][1000 genomes]
rs4791676	0.98[ASN][1000 genomes]
rs4791678	0.98[ASN][1000 genomes]
rs4792757	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4792760	0.97[ASN][1000 genomes]
rs4792761	0.98[ASN][1000 genomes]
rs4792762	0.98[ASN][1000 genomes]
rs5000166	0.98[ASN][1000 genomes]
rs55920274	0.98[ASN][1000 genomes]
rs56303920	0.98[ASN][1000 genomes]
rs57448521	0.98[ASN][1000 genomes]
rs58164310	0.98[ASN][1000 genomes]
rs59486407	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59594997	0.98[ASN][1000 genomes]
rs59826203	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072781	1.00[ASN][1000 genomes]
rs62072790	0.87[ASN][1000 genomes]
rs62072792	1.00[ASN][1000 genomes]
rs62072845	0.96[ASN][1000 genomes]
rs62073660	1.00[ASN][1000 genomes]
rs6502514	1.00[ASN][1000 genomes]
rs7208075	0.98[ASN][1000 genomes]
rs7213274	0.98[ASN][1000 genomes]
rs7217544	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7217717	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7218241	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7219632	1.00[ASN][1000 genomes]
rs7221518	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7222622	0.84[ASN][1000 genomes]
rs7222875	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7225641	0.98[ASN][1000 genomes]
rs7226328	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs72637355	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72637356	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72637357	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72637358	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72637359	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72637360	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72637361	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72637362	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72637363	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8065558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8068349	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8069286	0.80[ASN][1000 genomes]
rs8074285	1.00[ASN][1000 genomes]
rs8074464	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8074487	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs8075374	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs8075988	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8076849	0.98[ASN][1000 genomes]
rs8082225	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8082650	0.98[ASN][1000 genomes]
rs9889227	1.00[ASN][1000 genomes]
rs9890123	1.00[ASN][1000 genomes]
rs9890698	1.00[ASN][1000 genomes]
rs9891138	1.00[ASN][1000 genomes]
rs9894637	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9898888	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9899785	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9899919	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9901145	0.87[ASN][1000 genomes]
rs9904901	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9905710	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9906261	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9906728	1.00[ASN][1000 genomes]
rs9907785	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9908015	0.98[ASN][1000 genomes]
rs9908390	0.98[ASN][1000 genomes]
rs9909044	1.00[ASN][1000 genomes]
rs9909955	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9910087	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9910842	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9911162	0.98[ASN][1000 genomes]
rs9911524	0.88[CEU][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9911608	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9911677	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs9911820	0.98[ASN][1000 genomes]
rs9911851	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915121	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9916069	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9916258	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9916464	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9916819	1.00[CHB][hapmap];0.82[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	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
6	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16959869	RAI1	cis	cerebellum	SCAN
rs16959869	ZNF624	cis	cerebellum	SCAN
rs16959869	ZNF624	cis	multi-tissue	Pritchard

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16519800-16540000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr17:16520600-16533400	ZNF genes & repeats	Liver	Liver
3	chr17:16521200-16534200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr17:16522000-16540000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr17:16522600-16529000	ZNF genes & repeats	Primary T cells from cord blood	blood
6	chr17:16522800-16524000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
7	chr17:16522800-16528800	ZNF genes & repeats	Adipose Nuclei	Adipose
8	chr17:16523000-16525000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr17:16523000-16528600	ZNF genes & repeats	Fetal Brain Female	brain
10	chr17:16523000-16540400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr17:16523200-16532200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
12	chr17:16523200-16532200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr17:16523400-16524000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
14	chr17:16523400-16524000	ZNF genes & repeats	Placenta Amnion	Placenta Amnion
15	chr17:16523400-16524000	ZNF genes & repeats	Rectal Smooth Muscle	rectum
16	chr17:16523400-16524200	ZNF genes & repeats	Fetal Muscle Leg	muscle
17	chr17:16523400-16524400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
18	chr17:16523400-16524400	ZNF genes & repeats	Fetal Lung	lung
19	chr17:16523400-16534000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr17:16523400-16534000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
21	chr17:16523400-16537000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr17:16523400-16538400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr17:16523600-16524000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr17:16523600-16524000	ZNF genes & repeats	Brain Hippocampus Middle	brain
25	chr17:16523600-16524000	ZNF genes & repeats	Placenta	Placenta
26	chr17:16523600-16524000	ZNF genes & repeats	Psoas Muscle	Psoas
27	chr17:16523600-16524400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr17:16523600-16525000	ZNF genes & repeats	Brain Germinal Matrix	brain
29	chr17:16523800-16525600	Weak transcription	Brain Angular Gyrus	brain
30	chr17:16523800-16528400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
31	chr17:16523800-16528600	ZNF genes & repeats	Primary B cells from cord blood	blood

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