Variant report

Variant	rs1736211
Chromosome Location	chr17:17135422-17135423
allele	C/T
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	POLR2A	chr17:17135086-17135765	HepG2	liver:	n/a	n/a
2	HNF4A	chr17:17135340-17135607	HepG2	liver:	n/a	chr17:17135466-17135480 chr17:17135467-17135479 chr17:17135467-17135479 chr17:17135462-17135484 chr17:17135466-17135480 chr17:17135467-17135479 chr17:17135466-17135480 chr17:17135467-17135480 chr17:17135467-17135479 chr17:17135466-17135479 chr17:17135464-17135482 chr17:17135468-17135480
3	HNF4G	chr17:17135264-17135574	HepG2	liver:	n/a	chr17:17135466-17135480 chr17:17135467-17135479 chr17:17135467-17135479 chr17:17135462-17135484 chr17:17135466-17135480 chr17:17135467-17135479 chr17:17135466-17135480 chr17:17135467-17135480 chr17:17135467-17135479 chr17:17135466-17135479 chr17:17135464-17135482 chr17:17135468-17135480

No.	Distal block	Cell Line	Cell type
1	chr17:17131185..17133318-chr17:17133496..17135837,3	MCF-7	breast:
2	chr17:17121039..17123712-chr17:17133304..17136249,2	K562	blood:
3	chr17:17121039..17123215-chr17:17134749..17137620,2	K562	blood:
4	chr17:17133372..17136113-chr17:17139068..17140765,2	K562	blood:
5	chr17:17134971..17137251-chr17:17137733..17141244,3	K562	blood:

Variant related genes	Relation type
FLCN	TF binding region
ENSG00000154803	Chromatin interaction
ENSG00000266498	Chromatin interaction
ENSG00000264187	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11078378	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12453455	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs12600589	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12949822	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1630656	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1708617	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1708621	1.00[ASN][1000 genomes]
rs1708624	0.94[ASN][1000 genomes]
rs1708628	0.82[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs1736204	1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1736205	1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1736208	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1736209	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1736212	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1736216	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1736217	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1736218	0.83[ASN][1000 genomes]
rs1736221	0.99[ASN][1000 genomes]
rs2012954	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.92[ASN][1000 genomes]
rs2018781	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292527	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2349865	0.82[AMR][1000 genomes]
rs2472689	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs36079048	0.96[ASN][1000 genomes]
rs3803761	0.88[MEX][hapmap]
rs3866959	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs4399589	0.88[MEX][hapmap]
rs4985760	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs62066066	0.81[ASN][1000 genomes]
rs6502564	1.00[CHB][hapmap];0.82[CHD][hapmap];0.88[ASN][1000 genomes]
rs6502568	0.94[ASN][1000 genomes]
rs6502569	0.94[ASN][1000 genomes]
rs6502570	0.92[ASN][1000 genomes]
rs6502571	0.80[ASN][1000 genomes]
rs7217560	0.83[YRI][hapmap]
rs7218795	0.82[MEX][hapmap]
rs7220577	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs7221553	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7224598	0.93[ASN][1000 genomes]
rs7225876	0.94[ASN][1000 genomes]
rs8066090	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8080386	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9892352	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9894565	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1736211	FLCN	cis	cerebellum	SCAN
rs1736211	FLCN	cis	parietal	SCAN
rs1736211	TOM1L2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17113200-17136600	Strong transcription	Fetal Stomach	stomach
2	chr17:17113400-17136200	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr17:17113800-17137600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr17:17114000-17136200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr17:17114000-17136200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr17:17114000-17136400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr17:17114000-17136400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:17114000-17136400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr17:17114000-17136400	Strong transcription	Placenta	Placenta
10	chr17:17114000-17136600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr17:17114200-17136600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr17:17114400-17136200	Strong transcription	Primary T cells from cord blood	blood
13	chr17:17114400-17136200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr17:17114400-17136400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr17:17114400-17136600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr17:17114600-17136000	Strong transcription	Fetal Brain Female	brain
17	chr17:17114600-17136200	Strong transcription	NHLF	lung
18	chr17:17114600-17136400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr17:17114600-17136400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr17:17114600-17136400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr17:17114600-17136400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr17:17114600-17136400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr17:17114600-17136400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr17:17114600-17136600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr17:17114800-17136400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr17:17114800-17136400	Strong transcription	Osteobl	bone
27	chr17:17115000-17136200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr17:17115000-17136200	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr17:17115200-17139600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr17:17115400-17136200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr17:17115600-17136400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr17:17115800-17136000	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr17:17116000-17135800	Strong transcription	Thymus	Thymus
34	chr17:17116000-17136000	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr17:17116000-17136000	Strong transcription	Primary B cells from peripheral blood	blood
36	chr17:17116000-17136000	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr17:17116000-17136200	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr17:17116000-17136200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr17:17116000-17136200	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr17:17116000-17136400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr17:17116000-17136400	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr17:17116000-17136400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr17:17116000-17136400	Strong transcription	Dnd41	blood
44	chr17:17116200-17135800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr17:17116200-17136000	Strong transcription	Ovary	ovary
46	chr17:17116200-17136200	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr17:17116200-17136200	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr17:17116200-17136200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr17:17116200-17136200	Strong transcription	Brain Germinal Matrix	brain
50	chr17:17116200-17136200	Strong transcription	HSMMtube	muscle

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