Variant report

Variant	rs41319048
Chromosome Location	chr17:17059792-17059793
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	FOS	chr17:17059448-17059807	MCF10A-Er-Src	breast:	n/a	n/a
2	MAX	chr17:17059293-17059847	ECC-1	luminal epithelium:	n/a	n/a
3	RAD21	chr17:17059506-17059809	IMR90	lung:	n/a	n/a
4	MYC	chr17:17059392-17059807	MCF10A-Er-Src	breast:	n/a	n/a
5	NFIC	chr17:17059253-17059985	ECC-1	luminal epithelium:	n/a	n/a
6	ESR1	chr17:17059395-17059807	ECC-1	luminal epithelium:	n/a	n/a
7	TCF12	chr17:17059180-17059920	ECC-1	luminal epithelium:	n/a	chr17:17059563-17059573
8	POLR2A	chr17:17059296-17060288	U87	brain:	n/a	n/a
9	ESR1	chr17:17059379-17059838	ECC-1	luminal epithelium:	n/a	n/a
10	CEBPB	chr17:17059498-17059837	IMR90	lung:	n/a	n/a
11	EP300	chr17:17059136-17059944	ECC-1	luminal epithelium:	n/a	n/a
12	FOS	chr17:17059452-17059839	MCF10A-Er-Src	breast:	n/a	n/a
13	RCOR1	chr17:17058847-17060569	IMR90	lung:	n/a	n/a
14	POLR2A	chr17:17059456-17060257	U87	brain:	n/a	n/a
15	TEAD4	chr17:17059244-17059806	ECC-1	luminal epithelium:	n/a	n/a
16	FOS	chr17:17059437-17059832	MCF10A-Er-Src	breast:	n/a	n/a
17	NFIC	chr17:17059305-17059926	ECC-1	luminal epithelium:	n/a	n/a
18	MAX	chr17:17059268-17060124	ECC-1	luminal epithelium:	n/a	n/a
19	TCF12	chr17:17059218-17059953	ECC-1	luminal epithelium:	n/a	chr17:17059563-17059573

Variant related genes	Relation type
MPRIP	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12601193	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]
rs12601424	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12601453	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];0.97[ASN][1000 genomes]
rs12602196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12602675	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[MKK][hapmap];0.81[EUR][1000 genomes]
rs16961340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16961396	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271521	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292527	1.00[ASW][hapmap]
rs2292528	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[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];0.93[ASN][1000 genomes]
rs3744135	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]
rs3744142	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs3803762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3826304	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4078534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4316813	0.92[JPT][hapmap]
rs6502557	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.88[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];0.97[ASN][1000 genomes]
rs8072214	0.87[EUR][1000 genomes]
rs8076621	0.87[EUR][1000 genomes]
rs9908728	0.81[ASN][1000 genomes]
rs9909107	0.81[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	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
2	nsv524958	chr17:17029718-17060805	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41319048	FLCN	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17029800-17088400	Strong transcription	Dnd41	blood
2	chr17:17030000-17088000	Strong transcription	Duodenum Mucosa	Duodenum
3	chr17:17030400-17059800	Strong transcription	Fetal Intestine Small	intestine
4	chr17:17030400-17079200	Strong transcription	Sigmoid Colon	Sigmoid Colon
5	chr17:17030400-17089200	Strong transcription	Fetal Intestine Large	intestine
6	chr17:17031000-17078800	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr17:17031200-17067800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr17:17032000-17073800	Strong transcription	Fetal Lung	lung
9	chr17:17032200-17073600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr17:17034800-17072800	Strong transcription	Placenta Amnion	Placenta Amnion
11	chr17:17037200-17074200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:17038400-17093800	Strong transcription	Fetal Brain Female	brain
13	chr17:17044200-17083600	Strong transcription	Thymus	Thymus
14	chr17:17045000-17088400	Strong transcription	Brain Germinal Matrix	brain
15	chr17:17045200-17071600	Strong transcription	Primary B cells from cord blood	blood
16	chr17:17045200-17075600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr17:17045200-17093800	Strong transcription	Fetal Stomach	stomach
18	chr17:17045600-17071000	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr17:17045600-17072800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr17:17045800-17065600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr17:17046000-17059800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr17:17047600-17066200	Weak transcription	K562	blood
23	chr17:17050400-17073800	Strong transcription	Fetal Muscle Leg	muscle
24	chr17:17051000-17093200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr17:17053000-17078000	Strong transcription	Primary B cells from peripheral blood	blood
26	chr17:17053200-17060600	Genic enhancers	NHEK	skin
27	chr17:17053200-17060800	Genic enhancers	HMEC	breast
28	chr17:17053200-17061000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr17:17053200-17067200	Strong transcription	HepG2	liver
30	chr17:17053200-17072600	Strong transcription	Pancreas	Pancrea
31	chr17:17053200-17074600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr17:17053200-17088200	Strong transcription	Gastric	stomach
33	chr17:17053400-17062800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr17:17053600-17060600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr17:17054000-17062200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr17:17054200-17061800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr17:17054600-17064000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
38	chr17:17054600-17067000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr17:17054800-17087000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr17:17055200-17060000	Strong transcription	Stomach Mucosa	stomach
41	chr17:17055200-17065600	Strong transcription	GM12878-XiMat	blood
42	chr17:17055200-17073000	Strong transcription	Placenta	Placenta
43	chr17:17055200-17089400	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr17:17055400-17060200	Weak transcription	Small Intestine	intestine
45	chr17:17055400-17071400	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr17:17055400-17072400	Strong transcription	Ovary	ovary
47	chr17:17055600-17064000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr17:17055600-17092600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr17:17055800-17059800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr17:17055800-17061800	Strong transcription	Hela-S3	cervix

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