Variant report

Variant	rs17102960
Chromosome Location	chr1:79701220-79701221
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10489652	0.90[AFR][1000 genomes]
rs11162665	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11162689	1.00[AMR][1000 genomes]
rs11162690	1.00[AMR][1000 genomes]
rs12066657	1.00[AMR][1000 genomes]
rs12073676	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12073877	1.00[AMR][1000 genomes]
rs12077798	0.90[AFR][1000 genomes]
rs12080703	0.93[AFR][1000 genomes]
rs12080744	0.93[AFR][1000 genomes]
rs12081771	1.00[AMR][1000 genomes]
rs12084133	1.00[AMR][1000 genomes]
rs12089786	0.90[AFR][1000 genomes]
rs12090579	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091759	0.90[AFR][1000 genomes]
rs12092829	0.90[AFR][1000 genomes]
rs12094970	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17098591	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17102918	0.88[AFR][1000 genomes]
rs17102934	0.90[AFR][1000 genomes]
rs17102959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17102961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17102971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17103021	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57440705	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57890283	0.94[AFR][1000 genomes]
rs58229074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58899147	0.94[AFR][1000 genomes]
rs59133072	1.00[AMR][1000 genomes]
rs72941324	0.90[AFR][1000 genomes]
rs72941388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72943039	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72943069	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72945022	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72945043	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72945048	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72945064	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72945074	1.00[AMR][1000 genomes]
rs9943263	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491784	chr1:79146141-79853482	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv830326	chr1:79573379-79735667	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv871182	chr1:79614989-79822735	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv999471	chr1:79650363-79774433	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv870657	chr1:79701220-79890774	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79698400-79705000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:79700000-79702000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:79700200-79701800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:79700600-79702000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr1:79700600-79702200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:79700600-79702400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr1:79700800-79701400	Enhancers	NHDF-Ad	bronchial
8	chr1:79700800-79701800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr1:79700800-79702000	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr1:79700800-79702200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:79700800-79702200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:79701000-79701400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:79701000-79701400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:79701000-79701600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:79701000-79701600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr1:79701000-79701600	Flanking Active TSS	HUVEC	blood vessel
17	chr1:79701000-79701600	Flanking Active TSS	NH-A	brain
18	chr1:79701000-79701600	Flanking Active TSS	Osteobl	bone
19	chr1:79701000-79701800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:79701000-79701800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:79701000-79702000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:79701000-79702000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:79701200-79701400	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr1:79701200-79701400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:79701200-79701600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr1:79701200-79701600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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