Variant report

Variant	rs12600635
Chromosome Location	chr17:17142896-17142897
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	GATA1	chr17:17142760-17143627	PBDE	blood:	n/a	n/a
2	POLR2A	chr17:17142850-17143132	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:17142608..17144134-chr17:17146092..17148091,2	K562	blood:
2	chr17:17142459..17145077-chr17:17167559..17169849,2	K562	blood:
3	chr17:17141498..17143338-chr17:17206126..17208099,2	K562	blood:
4	chr17:17140695..17143255-chr17:17151117..17153823,2	MCF-7	breast:

Variant related genes	Relation type
FLCN	TF binding region
ENSG00000264187	TF binding region
ENSG00000226359	TF binding region
ENSG00000265109	TF binding region
ENSG00000266498	TF binding region
ENSG00000205309	Chromatin interaction
ENSG00000141030	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12601848	0.91[ASN][1000 genomes]
rs12602831	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12602871	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16961474	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16961493	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs16961507	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs2270180	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs2294155	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs34518797	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35534166	0.92[ASN][1000 genomes]
rs3744124	0.93[JPT][hapmap]
rs41283373	0.94[ASN][1000 genomes]
rs41337846	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41400246	0.84[AMR][1000 genomes]
rs41424546	0.88[AMR][1000 genomes]
rs55689224	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502565	0.96[ASN][1000 genomes]
rs7213351	0.91[ASN][1000 genomes]
rs7219012	0.95[ASN][1000 genomes]
rs7222600	0.93[JPT][hapmap]
rs7222697	0.91[ASN][1000 genomes]
rs7225789	0.90[ASN][1000 genomes]
rs7226227	0.90[ASN][1000 genomes]
rs8065774	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070995	0.95[ASN][1000 genomes]
rs8075526	0.97[ASN][1000 genomes]
rs8079562	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9890243	0.93[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9896078	1.00[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	esv1004208	chr17:17136933-17147885	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
IgG glycosylation	23382691	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12600635	FLCN	cis	lymphoblastoid	seeQTL
rs12600635	FLCN	cis	multi-tissue	Pritchard
rs12600635	PRPSAP2	cis	cerebellum	SCAN
rs12600635	PLD6	cis	cerebellum	SCAN
rs12600635	FLCN	cis	cerebellum	SCAN
rs12600635	NT5M	cis	Whole Blood	GTEx
rs12600635	COPS3	cis	multi-tissue	Pritchard
rs12600635	FLCN	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17141400-17145400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:17141400-17150400	Weak transcription	Aorta	Aorta
3	chr17:17141600-17143800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr17:17141600-17145200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr17:17141600-17145400	Weak transcription	Lung	lung
6	chr17:17141600-17148600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:17141600-17149000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr17:17141600-17149000	Weak transcription	Fetal Brain Female	brain
9	chr17:17141600-17149000	Weak transcription	Left Ventricle	heart
10	chr17:17141600-17149000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr17:17141600-17149200	Weak transcription	Brain Substantia Nigra	brain
12	chr17:17141600-17149200	Weak transcription	Right Ventricle	heart
13	chr17:17141600-17149200	Weak transcription	Spleen	Spleen
14	chr17:17141600-17149200	Weak transcription	HSMMtube	muscle
15	chr17:17141600-17149600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr17:17141600-17149800	Weak transcription	Esophagus	oesophagus
17	chr17:17141600-17149800	Weak transcription	Fetal Kidney	kidney
18	chr17:17141600-17150600	Weak transcription	Brain Angular Gyrus	brain
19	chr17:17141600-17161200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr17:17141800-17143000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr17:17141800-17143400	Enhancers	GM12878-XiMat	blood
22	chr17:17141800-17143600	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr17:17141800-17143800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr17:17141800-17145200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr17:17141800-17145200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr17:17141800-17148600	Weak transcription	Brain Hippocampus Middle	brain
27	chr17:17141800-17148600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr17:17141800-17148800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr17:17141800-17148800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr17:17141800-17148800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr17:17141800-17148800	Weak transcription	Fetal Stomach	stomach
32	chr17:17141800-17148800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr17:17141800-17149000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr17:17141800-17149000	Weak transcription	Primary B cells from cord blood	blood
35	chr17:17141800-17149000	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr17:17141800-17149000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr17:17141800-17149000	Weak transcription	Liver	Liver
38	chr17:17141800-17149000	Weak transcription	Brain Anterior Caudate	brain
39	chr17:17141800-17149000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr17:17141800-17149000	Weak transcription	Fetal Intestine Large	intestine
41	chr17:17141800-17149200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr17:17141800-17149200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr17:17141800-17149200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr17:17141800-17149200	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr17:17141800-17149200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr17:17141800-17149200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr17:17141800-17149200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr17:17141800-17149200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr17:17141800-17149200	Weak transcription	NH-A	brain
50	chr17:17141800-17149200	Weak transcription	NHDF-Ad	bronchial

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