Variant report

Variant	rs16962489
Chromosome Location	chr17:20829840-20829841
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	JUND	chr17:20829771-20830371	SK-N-SH	brain:	n/a	n/a
2	TEAD4	chr17:20829663-20830371	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr17:20829702-20830239	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr17:20829606-20830419	SK-N-SH	brain:	n/a	chr17:20829903-20829910
5	EP300	chr17:20829661-20830260	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr17:20829693-20830376	SK-N-SH	brain:	n/a	n/a
7	PBX3	chr17:20829743-20830222	SK-N-SH	brain:	n/a	n/a
8	MEF2A	chr17:20829762-20830272	SK-N-SH	brain:	n/a	chr17:20830081-20830096 chr17:20830122-20830133 chr17:20830081-20830096 chr17:20830119-20830135 chr17:20830120-20830135 chr17:20830120-20830135
9	PBX3	chr17:20829699-20830354	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr17:20829666-20830318	SK-N-SH	brain:	n/a	chr17:20829903-20829910
11	NFIC	chr17:20829621-20830331	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr17:20829756-20830219	SK-N-SH	brain:	n/a	n/a
13	MEF2A	chr17:20829740-20830356	SK-N-SH	brain:	n/a	chr17:20830081-20830096 chr17:20830122-20830133 chr17:20830081-20830096 chr17:20830119-20830135 chr17:20830120-20830135 chr17:20830120-20830135

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:20828074..20830327-chr17:20832191..20833842,2	K562	blood:
2	chr17:20828074..20830822-chr17:20831335..20835053,4	K562	blood:

Variant related genes	Relation type
ENSG00000233098	TF binding region
ENSG00000233098	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12602584	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs16962541	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs4405604	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4465653	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60606678	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61203188	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67192961	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67851864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916440	chr17:20171468-20839266	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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	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
3	esv3361931	chr17:20539962-20845258	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv962290	chr17:20826955-20830644	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv960384	chr17:20827680-20830644	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20812600-20830800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr17:20823400-20831600	Weak transcription	Colon Smooth Muscle	Colon
3	chr17:20823400-20833600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr17:20826000-20830800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr17:20826000-20837800	Weak transcription	K562	blood
6	chr17:20826400-20834800	Weak transcription	HepG2	liver
7	chr17:20826400-20837000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr17:20826600-20837200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr17:20826800-20835200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr17:20827000-20837000	Weak transcription	Hela-S3	cervix
11	chr17:20827200-20856200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:20828200-20833400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr17:20829000-20830600	Enhancers	HSMM	muscle
14	chr17:20829000-20830800	Enhancers	Osteobl	bone
15	chr17:20829000-20831000	Enhancers	NHDF-Ad	bronchial
16	chr17:20829000-20831200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr17:20829000-20831200	Enhancers	NHLF	lung
18	chr17:20829200-20830000	Enhancers	NH-A	brain
19	chr17:20829200-20830200	Enhancers	HSMMtube	muscle
20	chr17:20829200-20830600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr17:20829200-20834200	Enhancers	Rectal Smooth Muscle	rectum
22	chr17:20829200-20835800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr17:20829400-20830200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr17:20829400-20840600	Weak transcription	Ovary	ovary
25	chr17:20829600-20831200	Weak transcription	Right Atrium	heart
26	chr17:20829600-20833400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr17:20829800-20830000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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