Variant report

Variant	rs4985761
Chromosome Location	chr17:17179481-17179482
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	NR3C1	chr17:17179274-17179618	A549	lung:	n/a	chr17:17179293-17179307 chr17:17179292-17179308
2	POLR2A	chr17:17179444-17179504	K562	blood:	n/a	n/a
3	SPI1	chr17:17179301-17179720	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17177648..17180936-chr17:17181197..17184729,6	MCF-7	breast:
2	chr17:17179045..17181973-chr17:17206782..17208341,2	MCF-7	breast:

Variant related genes	Relation type
COPS3	TF binding region
ENSG00000141030	Chromatin interaction
ENSG00000205309	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1029829	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1029830	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1029832	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11652745	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12325679	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12450037	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452947	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12935953	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12937908	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12947291	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1613416	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1624963	0.89[ASN][1000 genomes]
rs1708618	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1708619	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1708620	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1708623	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1708626	0.96[ASN][1000 genomes]
rs1708627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1708629	0.96[ASN][1000 genomes]
rs1736200	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1736201	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1736202	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1736203	0.97[ASN][1000 genomes]
rs1736206	0.95[ASN][1000 genomes]
rs1736207	0.95[ASN][1000 genomes]
rs1736210	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1736213	0.95[ASN][1000 genomes]
rs1736214	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1736215	0.93[ASN][1000 genomes]
rs1736219	1.00[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3182911	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3853545	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4985705	0.95[JPT][hapmap]
rs4985752	0.88[ASW][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];1.00[YRI][hapmap]
rs4985759	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62066064	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7208065	0.95[JPT][hapmap]
rs7219248	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7220275	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8065832	0.96[CEU][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8070574	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8072402	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8072869	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9890657	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9894884	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9901894	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9903294	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9907107	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9908150	0.87[ASW][hapmap]

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	nsv833380	chr17:17088416-17241206	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1065811	chr17:17104760-17225204	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv833382	chr17:17124329-17305683	Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv469777	chr17:17127385-17272698	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv482546	chr17:17127385-17272698	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs4985761	FLCN	cis	lymphoblastoid	seeQTL
rs4985761	ZNF287	cis	cerebellum	SCAN
rs4985761	COPS3	cis	Whole Blood	GTEx
rs4985761	FLCN	cis	Adipose Subcutaneous	GTEx
rs4985761	FLCN	cis	multi-tissue	Pritchard
rs4985761	PLD6	cis	cerebellum	SCAN
rs4985761	FLCN	cis	Esophagus Mucosa	GTEx
rs4985761	FLCN	cis	Nerve Tibial	GTEx
rs4985761	FLCN	cis	Artery Aorta	GTEx
rs4985761	COPS3	cis	multi-tissue	Pritchard
rs4985761	FLCN	cis	Heart Left Ventricle	GTEx
rs4985761	FLCN	cis	Thyroid	GTEx
rs4985761	SMCR8	cis	cerebellum	SCAN
rs4985761	FLCN	cis	parietal	SCAN
rs4985761	FLCN	cis	Esophagus Muscularis	GTEx
rs4985761	FLCN	cis	lung	GTEx
rs4985761	FLCN	cis	Artery Tibial	GTEx
rs4985761	RAI1	cis	cerebellum	SCAN
rs4985761	M-RIP	cis	multi-tissue	Pritchard
rs4985761	FLCN	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17148600-17179600	Strong transcription	Fetal Muscle Trunk	muscle
2	chr17:17148600-17180000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr17:17148800-17179600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr17:17148800-17179600	Strong transcription	Fetal Muscle Leg	muscle
5	chr17:17148800-17179800	Strong transcription	Fetal Stomach	stomach
6	chr17:17148800-17180200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr17:17148800-17180400	Strong transcription	Fetal Thymus	thymus
8	chr17:17149000-17180800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr17:17149000-17181200	Strong transcription	Dnd41	blood
10	chr17:17149200-17179600	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr17:17149200-17179600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr17:17149200-17179800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr17:17149400-17179600	Strong transcription	Duodenum Mucosa	Duodenum
14	chr17:17149400-17179600	Strong transcription	Placenta	Placenta
15	chr17:17150000-17180000	Strong transcription	Primary T cells from cord blood	blood
16	chr17:17150200-17179800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr17:17155000-17179800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr17:17156800-17179600	Strong transcription	Liver	Liver
19	chr17:17157600-17179600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr17:17159800-17179600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr17:17160400-17181800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:17163600-17182600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr17:17163800-17180400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr17:17167200-17179600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr17:17167200-17179800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr17:17167200-17180200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr17:17169400-17179600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr17:17169800-17181400	Strong transcription	Fetal Intestine Small	intestine
29	chr17:17169800-17183200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr17:17171600-17182400	Weak transcription	Fetal Heart	heart
31	chr17:17171800-17183000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr17:17172000-17180600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr17:17173000-17179600	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr17:17174200-17182400	Weak transcription	HMEC	breast
35	chr17:17174400-17182600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr17:17174600-17181600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr17:17174600-17182400	Weak transcription	Psoas Muscle	Psoas
38	chr17:17174600-17182400	Weak transcription	Stomach Mucosa	stomach
39	chr17:17174600-17182400	Weak transcription	NHEK	skin
40	chr17:17174600-17183400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr17:17174800-17182600	Weak transcription	HSMMtube	muscle
42	chr17:17174800-17183000	Weak transcription	HSMM	muscle
43	chr17:17175600-17179600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr17:17175600-17179600	Strong transcription	Fetal Intestine Large	intestine
45	chr17:17175600-17180400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr17:17175600-17180600	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr17:17175800-17179800	Strong transcription	A549	lung
48	chr17:17175800-17180200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr17:17176600-17180400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr17:17177000-17180200	Strong transcription	HepG2	liver

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