Variant report

Variant	rs12601848
Chromosome Location	chr17:17185307-17185308
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	POLR2A	chr17:17183781-17185374	MCF10A-Er-Src	breast:	n/a	n/a
2	SIX5	chr17:17184082-17185388	A549	lung:	n/a	n/a
3	REST	chr17:17183485-17185580	H1-neurons	neurons:	n/a	chr17:17184022-17184032
4	MXI1	chr17:17183628-17185757	SK-N-SH	brain:	n/a	chr17:17184665-17184680 chr17:17184663-17184678
5	RFX5	chr17:17183740-17185531	SK-N-SH	brain:	n/a	chr17:17184664-17184679 chr17:17184664-17184679 chr17:17184664-17184679
6	POLR2A	chr17:17183818-17185379	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:17182421..17186483-chr17:17204152..17209830,5	MCF-7	breast:
2	chr17:17138280..17141930-chr17:17183181..17187644,4	MCF-7	breast:
3	chr17:17139508..17142367-chr17:17182538..17186121,3	MCF-7	breast:
4	chr17:17183415..17186229-chr17:17206165..17209020,3	MCF-7	breast:
5	chr17:17183059..17186537-chr17:17204352..17209458,5	K562	blood:
6	chr17:17132573..17135085-chr17:17184051..17185920,2	K562	blood:
7	chr17:17185180..17188227-chr17:17188770..17192072,3	K562	blood:
8	chr17:17181690..17186423-chr17:17204352..17210529,13	K562	blood:

Variant related genes	Relation type
COPS3	TF binding region
ENSG00000154803	Chromatin interaction
ENSG00000266498	Chromatin interaction
ENSG00000264187	Chromatin interaction
ENSG00000205309	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12600635	0.91[ASN][1000 genomes]
rs12602831	0.91[ASN][1000 genomes]
rs12602871	0.91[ASN][1000 genomes]
rs16961474	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16961493	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16961507	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2270180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294155	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34518797	0.91[ASN][1000 genomes]
rs35534166	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41283373	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41337846	0.91[ASN][1000 genomes]
rs55689224	0.91[ASN][1000 genomes]
rs6502565	0.87[ASN][1000 genomes]
rs7213351	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219012	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7222697	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7225789	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7226227	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8065774	0.91[ASN][1000 genomes]
rs8070995	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8075526	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8079562	0.91[ASN][1000 genomes]
rs9890243	0.93[ASN][1000 genomes]
rs9896078	0.92[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	nsv9499	chr17:17181611-17187670	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12601848	FLCN	cis	Artery Tibial	GTEx
rs12601848	NT5M	cis	Whole Blood	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17183200-17185400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr17:17183200-17185400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr17:17183200-17185400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr17:17183400-17185400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr17:17183400-17185400	Active TSS	Brain Anterior Caudate	brain
6	chr17:17183400-17185400	Active TSS	Fetal Kidney	kidney
7	chr17:17183600-17185400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr17:17183600-17185400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr17:17183800-17185400	Active TSS	Fetal Brain Male	brain
10	chr17:17184600-17185400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr17:17184800-17185400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:17184800-17185400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr17:17184800-17185400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr17:17184800-17185400	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr17:17184800-17185400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr17:17184800-17185400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr17:17184800-17185400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr17:17184800-17185400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr17:17184800-17185400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr17:17184800-17185400	Flanking Active TSS	Fetal Heart	heart
21	chr17:17184800-17185400	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr17:17184800-17185400	Flanking Active TSS	A549	lung
23	chr17:17184800-17185400	Flanking Active TSS	GM12878-XiMat	blood
24	chr17:17184800-17185400	Flanking Active TSS	NH-A	brain
25	chr17:17184800-17185400	Flanking Active TSS	NHLF	lung
26	chr17:17184800-17185400	Flanking Active TSS	Osteobl	bone
27	chr17:17184800-17185600	Flanking Active TSS	Dnd41	blood
28	chr17:17184800-17185600	Flanking Active TSS	K562	blood
29	chr17:17185000-17185400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr17:17185000-17185400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr17:17185000-17185400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr17:17185000-17185400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr17:17185000-17185400	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr17:17185000-17185400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr17:17185000-17185400	Flanking Active TSS	NHDF-Ad	bronchial
36	chr17:17185000-17185600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr17:17185000-17185600	Active TSS	HepG2	liver
38	chr17:17185200-17185400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr17:17185200-17185400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr17:17185200-17185400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr17:17185200-17185400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr17:17185200-17185400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr17:17185200-17185400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr17:17185200-17185400	Enhancers	Primary B cells from cord blood	blood
45	chr17:17185200-17185400	Enhancers	Primary B cells from peripheral blood	blood
46	chr17:17185200-17185400	Enhancers	Primary T cells from cord blood	blood
47	chr17:17185200-17185400	Enhancers	Primary T cells fromperipheralblood	blood
48	chr17:17185200-17185400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr17:17185200-17185400	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr17:17185200-17185400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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