Variant report

Variant	rs12601193
Chromosome Location	chr17:17013189-17013190
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16283299..16285911-chr17:17011772..17013387,2	MCF-7	breast:
2	chr17:17011485..17013573-chr17:17019778..17021863,2	MCF-7	breast:
3	chr17:16944526..16947227-chr17:17010435..17013618,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133030	Chromatin interaction
ENSG00000170315	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12601424	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12601453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12602196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12602675	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs16961340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16961396	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2271521	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292527	1.00[ASW][hapmap]
rs2292528	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3744124	1.00[CEU][hapmap]
rs3744126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3744135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3744142	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs3803762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3826304	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4078534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41319048	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4316813	0.92[JPT][hapmap]
rs4328504	0.81[ASN][1000 genomes]
rs6502557	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs6502565	1.00[CEU][hapmap]
rs7222600	1.00[CEU][hapmap]
rs8064771	0.92[JPT][hapmap]
rs8069241	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8072214	0.87[EUR][1000 genomes]
rs8076621	0.87[EUR][1000 genomes]
rs9908728	0.84[ASN][1000 genomes]
rs9909107	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059280	chr17:16975059-17017957	Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv907728	chr17:17013189-17095487	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12601193	FLCN	cis	lymphoblastoid	seeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16986800-17013600	Weak transcription	HUVEC	blood vessel
2	chr17:16997000-17016600	Enhancers	Left Ventricle	heart
3	chr17:16998200-17016200	Enhancers	Fetal Heart	heart
4	chr17:16998600-17015400	Genic enhancers	Fetal Muscle Leg	muscle
5	chr17:16998600-17016600	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr17:17000200-17018200	Weak transcription	NH-A	brain
7	chr17:17002600-17023200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:17004000-17014000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr17:17006200-17033000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr17:17006800-17016600	Enhancers	Right Ventricle	heart
11	chr17:17007400-17014200	Enhancers	Colon Smooth Muscle	Colon
12	chr17:17007400-17016600	Enhancers	Pancreas	Pancrea
13	chr17:17007600-17016600	Enhancers	Right Atrium	heart
14	chr17:17007800-17014000	Enhancers	Fetal Thymus	thymus
15	chr17:17007800-17015400	Enhancers	Psoas Muscle	Psoas
16	chr17:17007800-17021000	Weak transcription	HepG2	liver
17	chr17:17008000-17017200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr17:17008400-17014800	Enhancers	NHDF-Ad	bronchial
19	chr17:17008400-17015000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr17:17008400-17016600	Enhancers	Placenta	Placenta
21	chr17:17009200-17015400	Enhancers	Ovary	ovary
22	chr17:17009200-17025200	Enhancers	Brain Anterior Caudate	brain
23	chr17:17009400-17013600	Enhancers	Brain Substantia Nigra	brain
24	chr17:17009400-17013800	Enhancers	Duodenum Mucosa	Duodenum
25	chr17:17009400-17015000	Enhancers	Adipose Nuclei	Adipose
26	chr17:17009400-17016000	Enhancers	Esophagus	oesophagus
27	chr17:17009400-17016200	Genic enhancers	A549	lung
28	chr17:17009400-17016600	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr17:17009400-17020600	Enhancers	Lung	lung
30	chr17:17009600-17014400	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr17:17009600-17015400	Enhancers	Brain Hippocampus Middle	brain
32	chr17:17009600-17015400	Genic enhancers	Fetal Intestine Small	intestine
33	chr17:17009800-17013600	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr17:17009800-17014200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr17:17009800-17014200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr17:17009800-17014800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr17:17009800-17015000	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr17:17009800-17015600	Genic enhancers	HSMM	muscle
39	chr17:17009800-17017000	Enhancers	Brain Angular Gyrus	brain
40	chr17:17010000-17014000	Enhancers	Brain Cingulate Gyrus	brain
41	chr17:17010000-17014000	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr17:17010000-17014200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr17:17010000-17014200	Enhancers	Spleen	Spleen
44	chr17:17010000-17014400	Genic enhancers	NHEK	skin
45	chr17:17010000-17032000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr17:17010200-17013600	Enhancers	NHLF	lung
47	chr17:17010200-17014000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr17:17010200-17014000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr17:17010200-17014400	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr17:17010200-17014800	Enhancers	Rectal Mucosa Donor 31	rectum

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