Variant report

Variant	rs3813766
Chromosome Location	chr17:16557606-16557607
allele	A/C
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	YY1	chr17:16556446-16557629	SK-N-SH	brain:	n/a	chr17:16557137-16557147 chr17:16557036-16557045
2	SIX5	chr17:16556611-16557718	A549	lung:	n/a	n/a
3	MAX	chr17:16556407-16557614	HCT-116	colon:	n/a	chr17:16556820-16556830
4	HCFC1	chr17:16556175-16558257	Hela-S3	cervix:	n/a	n/a
5	REST	chr17:16555981-16557853	H1-neurons	neurons:	n/a	n/a
6	ETS1	chr17:16556775-16557650	A549	lung:	n/a	chr17:16557205-16557218
7	SP1	chr17:16556344-16557653	HCT-116	colon:	n/a	chr17:16556994-16557004 chr17:16556953-16556963 chr17:16557239-16557248 chr17:16557237-16557249 chr17:16556952-16556964 chr17:16557243-16557250 chr17:16557237-16557249 chr17:16556952-16556964 chr17:16557238-16557247
8	KAP1	chr17:16556806-16557758	U2OS	brain:	n/a	n/a
9	E2F6	chr17:16556454-16557630	A549	lung:	n/a	chr17:16557119-16557130 chr17:16557118-16557130 chr17:16557181-16557190 chr17:16557036-16557045 chr17:16557054-16557064
10	POLR2A	chr17:16556055-16557635	H1-neurons	neurons:	n/a	n/a
11	MAZ	chr17:16556416-16557922	IMR90	lung:	n/a	chr17:16556820-16556830
12	SP1	chr17:16556633-16557638	A549	lung:	n/a	chr17:16556994-16557004 chr17:16556953-16556963 chr17:16557239-16557248 chr17:16557237-16557249 chr17:16556952-16556964 chr17:16557243-16557250 chr17:16557237-16557249 chr17:16556952-16556964 chr17:16557238-16557247

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16341411..16344243-chr17:16555470..16557634,2	K562	blood:
2	chr17:16556241..16557924-chr4:3075466..3077603,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC144A-2	chr17:16557398-16558101	ENSG00000264765.1

Variant related genes	Relation type
ZNF624	TF binding region
ENSG00000175061	Chromatin interaction
ENSG00000251075	Chromatin interaction
ENSG00000197386	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11654767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11656972	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11658427	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11658964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16959888	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66553135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72835914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72835919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72835920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72835926	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72835927	0.81[AMR][1000 genomes]
rs9889590	0.90[EUR][1000 genomes]
rs9916655	0.89[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	esv2758442	chr17:16527056-16817437	Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	esv2758676	chr17:16527056-16817437	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv427991	chr17:16527056-16817437	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv907720	chr17:16557606-16758204	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16556200-16557800	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr17:16556200-16557800	Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr17:16556200-16558000	Active TSS	Brain Cingulate Gyrus	brain
4	chr17:16556400-16557800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr17:16556400-16557800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr17:16556400-16557800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr17:16556400-16557800	Active TSS	Brain Anterior Caudate	brain
8	chr17:16556600-16558000	Active TSS	Stomach Smooth Muscle	stomach
9	chr17:16556800-16557800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr17:16557000-16558000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr17:16557200-16557800	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr17:16557200-16558000	Flanking Active TSS	Dnd41	blood
13	chr17:16557200-16561800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr17:16557400-16557800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr17:16557400-16557800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr17:16557400-16557800	Flanking Active TSS	Colon Smooth Muscle	Colon
17	chr17:16557400-16557800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr17:16557400-16557800	Flanking Active TSS	A549	lung
19	chr17:16557400-16558000	Flanking Active TSS	Brain Hippocampus Middle	brain
20	chr17:16557400-16558000	Flanking Active TSS	Brain Substantia Nigra	brain
21	chr17:16557400-16570000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:16557600-16557800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr17:16557600-16557800	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr17:16557600-16557800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr17:16557600-16557800	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
26	chr17:16557600-16557800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr17:16557600-16557800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr17:16557600-16557800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr17:16557600-16557800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
30	chr17:16557600-16557800	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr17:16557600-16557800	Flanking Active TSS	Brain Angular Gyrus	brain
32	chr17:16557600-16557800	Enhancers	Fetal Brain Female	brain
33	chr17:16557600-16557800	Enhancers	Fetal Heart	heart
34	chr17:16557600-16557800	Enhancers	Fetal Lung	lung
35	chr17:16557600-16557800	Enhancers	Fetal Stomach	stomach
36	chr17:16557600-16557800	Enhancers	Rectal Smooth Muscle	rectum
37	chr17:16557600-16557800	Enhancers	HepG2	liver
38	chr17:16557600-16557800	Active TSS	HMEC	breast
39	chr17:16557600-16557800	Enhancers	NHEK	skin
40	chr17:16557600-16558000	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr17:16557600-16558000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr17:16557600-16558000	Enhancers	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links