Variant report

Variant	rs9896109
Chromosome Location	chr17:20859147-20859148
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr17:20859116-20859295	GM12878	blood:	n/a	n/a
2	USF1	chr17:20858793-20859232	A549	lung:	n/a	n/a
3	STAT3	chr17:20858699-20859666	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr17:20858284-20859753	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr17:20858474-20859648	MCF10A-Er-Src	breast:	n/a	chr17:20858585-20858608
6	STAT3	chr17:20858714-20859467	MCF10A-Er-Src	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DHRS7B-5	chr17:20859130-20859666	ENSG00000233098.3
2	lnc-DHRS7B-5	chr17:20857205-20859807	NONHSAT146865
3	lnc-DHRS7B-5	chr17:20859130-20859666	ENSG00000233098.4

Variant related genes	Relation type
ENSG00000233098	TF binding region
ENSG00000244456	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11204325	0.82[JPT][hapmap]
rs11204326	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204327	0.90[ASN][1000 genomes]
rs11650623	0.89[ASN][1000 genomes]
rs11653213	0.81[ASN][1000 genomes]
rs11655512	0.82[JPT][hapmap]
rs11656525	0.82[ASN][1000 genomes]
rs11656837	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11658389	0.82[ASN][1000 genomes]
rs11658722	0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs11658791	0.82[ASN][1000 genomes]
rs16962469	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4545877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4985936	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4985940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4985943	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4985944	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62055511	0.84[ASN][1000 genomes]
rs62056765	0.82[ASN][1000 genomes]
rs62056768	0.82[ASN][1000 genomes]
rs7215006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7216145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7218520	0.84[CHB][hapmap]
rs7221189	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7226143	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7501524	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7501525	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8080233	0.84[ASN][1000 genomes]
rs9325900	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9914432	0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs9972887	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751619	chr17:20462908-20914156	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv3330516	chr17:20572433-20862663	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1064365	chr17:20801739-20890716	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	nsv574597	chr17:20802778-20872331	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv527161	chr17:20814766-20872331	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv457706	chr17:20814766-20872331	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv574598	chr17:20814766-20872331	Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
10	nsv2006	chr17:20846763-20892730	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9896109	RP11-344E13.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20835600-20869000	Weak transcription	HepG2	liver
2	chr17:20847800-20869400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:20848200-20859400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr17:20848200-20860600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr17:20848200-20864600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr17:20848200-20872200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr17:20848200-20896600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:20848400-20865000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr17:20852800-20882600	Weak transcription	K562	blood
10	chr17:20855200-20860200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr17:20857800-20859200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr17:20857800-20859600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr17:20857800-20859800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr17:20857800-20859800	Enhancers	Fetal Lung	lung
15	chr17:20857800-20867600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:20858000-20859200	Weak transcription	Psoas Muscle	Psoas
17	chr17:20858000-20859200	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr17:20858000-20859600	Enhancers	Muscle Satellite Cultured Cells	--
19	chr17:20858000-20859800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr17:20858000-20859800	Enhancers	HSMM	muscle
21	chr17:20858200-20859400	Enhancers	Liver	Liver
22	chr17:20858200-20859400	Enhancers	Osteobl	bone
23	chr17:20858200-20859600	Enhancers	Fetal Intestine Large	intestine
24	chr17:20858200-20859600	Enhancers	Fetal Muscle Leg	muscle
25	chr17:20858200-20859600	Enhancers	Ovary	ovary
26	chr17:20858200-20859600	Enhancers	Pancreas	Pancrea
27	chr17:20858200-20859600	Enhancers	NHDF-Ad	bronchial
28	chr17:20858200-20860200	Enhancers	NHEK	skin
29	chr17:20858400-20859400	Enhancers	Stomach Mucosa	stomach
30	chr17:20858400-20859800	Enhancers	HMEC	breast
31	chr17:20858400-20860000	Enhancers	Colon Smooth Muscle	Colon
32	chr17:20858400-20864400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr17:20858600-20859800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr17:20858600-20860200	Enhancers	Hela-S3	cervix
35	chr17:20858800-20859200	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr17:20858800-20859400	Enhancers	Adipose Nuclei	Adipose
37	chr17:20858800-20860200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr17:20859000-20859400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr17:20859000-20859400	Flanking Active TSS	HSMMtube	muscle
40	chr17:20859000-20859600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr17:20859000-20859600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr17:20859000-20859600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr17:20859000-20859600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr17:20859000-20859600	Enhancers	Fetal Stomach	stomach
45	chr17:20859000-20881800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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