Variant report

Variant	rs16975717
Chromosome Location	chr15:45135358-45135359
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11070436	0.90[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs11543459	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11630472	0.83[ASN][1000 genomes]
rs12050579	0.81[ASN][1000 genomes]
rs12592076	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12592596	0.83[ASN][1000 genomes]
rs12593337	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12595073	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12595326	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12595603	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1288097	0.83[ASN][1000 genomes]
rs1288098	0.94[ASN][1000 genomes]
rs1288103	0.88[ASN][1000 genomes]
rs1288105	0.90[ASN][1000 genomes]
rs1290485	0.90[ASN][1000 genomes]
rs16975906	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2468044	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2470906	0.90[ASN][1000 genomes]
rs270821	1.00[CEU][hapmap]
rs28497325	0.94[ASN][1000 genomes]
rs2899129	0.83[ASN][1000 genomes]
rs2948905	0.90[ASN][1000 genomes]
rs2948906	0.91[ASN][1000 genomes]
rs2948909	0.94[ASN][1000 genomes]
rs3110656	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3110661	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34561910	0.83[ASN][1000 genomes]
rs4378566	0.84[ASN][1000 genomes]
rs4635283	0.83[ASN][1000 genomes]
rs4775268	0.83[ASN][1000 genomes]
rs4775279	0.83[ASN][1000 genomes]
rs67440818	0.83[ASN][1000 genomes]
rs7162958	0.81[ASN][1000 genomes]
rs7165296	1.00[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs7165793	0.94[ASN][1000 genomes]
rs7175998	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs735480	0.83[ASN][1000 genomes]
rs74009451	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8026050	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8026423	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8027024	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8040024	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv832990	chr15:44990765-45162714	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
5	nsv1048668	chr15:45094019-45284278	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1050650	chr15:45096539-45229584	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2753798	chr15:45100852-45145764	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1048867	chr15:45100852-45289756	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	esv2757599	chr15:45100852-45383620	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv1036204	chr15:45105374-45284278	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv1047353	chr15:45105374-45289756	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv1040940	chr15:45105374-45300844	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	esv2753133	chr15:45105876-45268182	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	esv34494	chr15:45105876-45268208	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv1041613	chr15:45111367-45284278	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv1053041	chr15:45117399-45289756	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	esv2761871	chr15:45117411-45137994	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv1040140	chr15:45121635-45289756	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	nsv904181	chr15:45127793-45216343	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	esv3336976	chr15:45129810-45151008	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	esv3499684	chr15:45130660-45140008	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region	1 gene(s)	inside rSNPs	diseases
22	esv3499686	chr15:45130660-45140008	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
23	esv2581792	chr15:45131160-45146153	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	esv3499074	chr15:45131769-45145923	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	esv1806803	chr15:45131787-45145767	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv442373	chr15:45131787-45145767	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	esv2763097	chr15:45131787-45149740	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
28	esv16490	chr15:45131798-45145856	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	esv3499076	chr15:45131856-45145844	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
30	nsv9257	chr15:45131972-45146081	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
31	nsv977709	chr15:45134834-45136882	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
32	esv2573192	chr15:45134952-45144769	Enhancers Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16975717	HPS3	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45134400-45141000	Weak transcription	HepG2	liver
2	chr15:45135000-45135400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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