Variant report

Variant	rs12949822
Chromosome Location	chr17:17141330-17141331
allele	G/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	SIX5	chr17:17139986-17141436	A549	lung:	n/a	n/a
2	SP1	chr17:17140044-17141330	A549	lung:	n/a	chr17:17140292-17140301 chr17:17140291-17140303 chr17:17140292-17140301 chr17:17140366-17140379 chr17:17140292-17140302 chr17:17140293-17140302 chr17:17140292-17140302 chr17:17140291-17140303
3	POLR2A	chr17:17140227-17141845	GM12891	blood:	n/a	n/a
4	POLR2A	chr17:17140111-17141339	MCF-7	breast:	n/a	n/a
5	POLR2A	chr17:17139123-17141667	K562	blood:	n/a	n/a
6	PML	chr17:17140083-17141385	GM12878	blood:	n/a	n/a
7	SP1	chr17:17139741-17141337	A549	lung:	n/a	chr17:17140292-17140301 chr17:17140291-17140303 chr17:17140292-17140301 chr17:17140366-17140379 chr17:17140292-17140302 chr17:17140293-17140302 chr17:17140292-17140302 chr17:17140291-17140303
8	GATA3	chr17:17140034-17141350	A549	lung:	n/a	n/a
9	POLR2A	chr17:17140045-17141330	MCF-7	breast:	n/a	n/a
10	POLR2A	chr17:17140149-17141344	ProgFib	skin:	n/a	n/a
11	SIN3AK20	chr17:17139271-17141330	MCF-7	breast:	n/a	n/a
12	E2F6	chr17:17140196-17141364	A549	lung:	n/a	n/a
13	SP1	chr17:17140164-17141331	HCT-116	colon:	n/a	chr17:17140292-17140301 chr17:17140291-17140303 chr17:17140292-17140301 chr17:17140366-17140379 chr17:17140292-17140302 chr17:17140293-17140302 chr17:17140292-17140302 chr17:17140291-17140303
14	MAX	chr17:17139727-17141344	ECC-1	luminal epithelium:	n/a	chr17:17140995-17141004 chr17:17140995-17141004 chr17:17140995-17141004 chr17:17140028-17140037
15	POLR2A	chr17:17139782-17141358	GM12892	blood:	n/a	n/a
16	CHD1	chr17:17138651-17141410	IMR90	lung:	n/a	n/a
17	MAX	chr17:17139484-17141836	A549	lung:	n/a	chr17:17140995-17141004 chr17:17140995-17141004 chr17:17140995-17141004 chr17:17140028-17140037
18	USF1	chr17:17140164-17141366	HCT-116	colon:	n/a	chr17:17140993-17141006 chr17:17140989-17141010 chr17:17140996-17141005 chr17:17140995-17141004 chr17:17140994-17141003 chr17:17140995-17141004
19	CEBPB	chr17:17140357-17141348	A549	lung:	n/a	n/a
20	SREBP1	chr17:17139830-17141459	GM12878	blood:	n/a	chr17:17140995-17141004 chr17:17140994-17141004 chr17:17140995-17141004 chr17:17140995-17141005
21	POLR2A	chr17:17139751-17141429	U87	brain:	n/a	n/a
22	FOXM1	chr17:17140204-17141377	GM12878	blood:	n/a	n/a
23	POLR2A	chr17:17140103-17141354	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr17:17139751-17141432	U87	brain:	n/a	n/a
25	REST	chr17:17139654-17141359	A549	lung:	n/a	chr17:17140543-17140556 chr17:17140561-17140579 chr17:17140475-17140488
26	POLR2A	chr17:17139984-17141369	GM12878	blood:	n/a	n/a
27	POLR2A	chr17:17140145-17141730	HEK293	kidney:	n/a	n/a
28	JUND	chr17:17139484-17141498	SK-N-SH	brain:	n/a	n/a
29	MAX	chr17:17139585-17141381	HCT-116	colon:	n/a	chr17:17140995-17141004 chr17:17140995-17141004 chr17:17140995-17141004 chr17:17140028-17140037
30	POLR2A	chr17:17140063-17141377	HUVEC	blood vessel:	n/a	n/a
31	HCFC1	chr17:17138750-17141455	Hela-S3	cervix:	n/a	n/a
32	TCF12	chr17:17139610-17141502	A549	lung:	n/a	chr17:17140978-17140985 chr17:17140426-17140436 chr17:17140252-17140259
33	POLR2A	chr17:17140075-17141361	SK-N-MC	brain:	n/a	n/a
34	POLR2A	chr17:17140124-17141332	Hela-S3	cervix:	n/a	n/a
35	NRF1	chr17:17140366-17141349	SK-N-SH	brain:	n/a	chr17:17141061-17141072 chr17:17141062-17141071
36	TAF1	chr17:17139957-17141386	A549	lung:	n/a	n/a
37	JUND	chr17:17140113-17141344	HCT-116	colon:	n/a	n/a
38	MAX	chr17:17140025-17141362	A549	lung:	n/a	chr17:17140995-17141004 chr17:17140995-17141004 chr17:17140995-17141004 chr17:17140028-17140037
39	POLR2A	chr17:17140940-17141332	HL-60	blood:	n/a	n/a
40	POLR2A	chr17:17140170-17141340	GM19193	blood:	n/a	n/a
41	REST	chr17:17139511-17141548	H1-neurons	neurons:	n/a	chr17:17140543-17140556 chr17:17140561-17140579 chr17:17140475-17140488
42	GTF3C2	chr17:17140842-17141506	Hela-S3	cervix:	n/a	n/a
43	MXI1	chr17:17139428-17141910	SK-N-SH	brain:	n/a	n/a
44	MAX	chr17:17140119-17141343	HCT-116	colon:	n/a	chr17:17140995-17141004 chr17:17140995-17141004 chr17:17140995-17141004
45	POLR2A	chr17:17140136-17141347	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr17:17139977-17141421	PFSK-1	brain:	n/a	n/a
47	POLR2A	chr17:17140724-17141373	GM12892	blood:	n/a	n/a
48	USF1	chr17:17139730-17141344	HCT-116	colon:	n/a	chr17:17140993-17141006 chr17:17140989-17141010 chr17:17140996-17141005 chr17:17140995-17141004 chr17:17140994-17141003 chr17:17140995-17141004
49	POLR2A	chr17:17140222-17141334	GM12878	blood:	n/a	n/a
50	ELF1	chr17:17140118-17141438	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:17138742..17142464-chr17:17205516..17208012,3	MCF-7	breast:
2	chr17:17139508..17142367-chr17:17182538..17186121,3	MCF-7	breast:
3	chr17:17139354..17141733-chr17:17143268..17148053,6	MCF-7	breast:
4	chr17:17140058..17141717-chr17:17149806..17152339,2	MCF-7	breast:
5	chr17:17135534..17137524-chr17:17138995..17141355,2	MCF-7	breast:
6	chr17:17107449..17109941-chr17:17138935..17142587,4	MCF-7	breast:
7	chr17:17126262..17128515-chr17:17140252..17142748,2	MCF-7	breast:
8	chr17:17103497..17105821-chr17:17140669..17142216,2	K562	blood:
9	chr17:17138850..17142014-chr17:17149192..17152269,3	K562	blood:
10	chr17:17139597..17142266-chr17:17398056..17400275,2	MCF-7	breast:
11	chr17:17138280..17141930-chr17:17183181..17187644,4	MCF-7	breast:
12	chr17:17140695..17143255-chr17:17151117..17153823,2	MCF-7	breast:
13	chr17:17139635..17142575-chr17:17144486..17149716,4	K562	blood:

Variant related genes	Relation type
ENSG00000264187	TF binding region
ENSG00000226359	TF binding region
FLCN	TF binding region
ENSG00000266498	TF binding region
ENSG00000265109	TF binding region
ENSG00000141030	Chromatin interaction
ENSG00000226359	Chromatin interaction
ENSG00000265109	Chromatin interaction
ENSG00000179598	Chromatin interaction
ENSG00000205309	Chromatin interaction
ENSG00000154803	Chromatin interaction
ENSG00000108551	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11078378	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12453455	0.81[ASN][1000 genomes]
rs12600589	0.80[ASN][1000 genomes]
rs1630656	0.81[ASN][1000 genomes]
rs1708617	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1708621	0.81[ASN][1000 genomes]
rs1708624	0.81[ASN][1000 genomes]
rs1708628	0.85[AFR][1000 genomes]
rs1736204	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1736205	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1736208	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1736209	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1736211	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1736212	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1736216	0.81[ASN][1000 genomes]
rs1736217	0.81[ASN][1000 genomes]
rs1736221	0.80[ASN][1000 genomes]
rs2018781	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2349865	0.82[AMR][1000 genomes]
rs3866959	0.81[ASN][1000 genomes]
rs4985760	0.81[ASN][1000 genomes]
rs6502564	0.82[ASN][1000 genomes]
rs6502568	0.81[ASN][1000 genomes]
rs6502569	0.81[ASN][1000 genomes]
rs7220577	0.81[ASN][1000 genomes]
rs7224598	0.80[ASN][1000 genomes]
rs7225876	0.81[ASN][1000 genomes]
rs8066090	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8080386	0.80[ASN][1000 genomes]
rs9892352	0.81[ASN][1000 genomes]
rs9894565	0.81[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12949822	FLCN	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17138400-17141400	Active TSS	Fetal Intestine Large	intestine
2	chr17:17138400-17142200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr17:17138600-17141600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr17:17138600-17141800	Active TSS	NHDF-Ad	bronchial
5	chr17:17138800-17141600	Active TSS	HSMMtube	muscle
6	chr17:17139000-17142400	Active TSS	Ovary	ovary
7	chr17:17139200-17141600	Active TSS	Brain Angular Gyrus	brain
8	chr17:17139200-17141800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr17:17139400-17141400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr17:17139400-17141400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr17:17139400-17141400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr17:17139400-17141400	Active TSS	Aorta	Aorta
13	chr17:17139400-17141400	Active TSS	Lung	lung
14	chr17:17139400-17141400	Active TSS	Right Ventricle	heart
15	chr17:17139400-17141600	Active TSS	Brain Cingulate Gyrus	brain
16	chr17:17139400-17141600	Active TSS	Left Ventricle	heart
17	chr17:17139400-17141600	Active TSS	Pancreas	Pancrea
18	chr17:17139400-17141600	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr17:17139400-17141800	Active TSS	Muscle Satellite Cultured Cells	--
20	chr17:17139400-17141800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr17:17139400-17141800	Active TSS	Colon Smooth Muscle	Colon
22	chr17:17139400-17141800	Active TSS	Psoas Muscle	Psoas
23	chr17:17139400-17141800	Active TSS	NHLF	lung
24	chr17:17139400-17142000	Active TSS	H1 Cell Line	embryonic stem cell
25	chr17:17139400-17142000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr17:17139400-17142200	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr17:17139400-17142200	Active TSS	Gastric	stomach
28	chr17:17139600-17141400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr17:17139600-17141400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr17:17139600-17141400	Active TSS	Fetal Stomach	stomach
31	chr17:17139600-17141400	Active TSS	A549	lung
32	chr17:17139600-17141600	Active TSS	Brain Anterior Caudate	brain
33	chr17:17139600-17141600	Active TSS	Fetal Kidney	kidney
34	chr17:17139600-17141600	Active TSS	Small Intestine	intestine
35	chr17:17139600-17141600	Active TSS	Stomach Mucosa	stomach
36	chr17:17139600-17141800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr17:17139600-17141800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr17:17139600-17141800	Active TSS	Brain Hippocampus Middle	brain
39	chr17:17139600-17141800	Active TSS	Rectal Smooth Muscle	rectum
40	chr17:17139600-17142200	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr17:17139600-17142200	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr17:17139800-17141400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr17:17139800-17141400	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr17:17139800-17141400	Active TSS	Fetal Heart	heart
45	chr17:17139800-17141400	Active TSS	Fetal Muscle Leg	muscle
46	chr17:17139800-17141600	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr17:17139800-17141600	Active TSS	Brain Substantia Nigra	brain
48	chr17:17139800-17141600	Active TSS	Esophagus	oesophagus
49	chr17:17139800-17141600	Active TSS	GM12878-XiMat	blood
50	chr17:17139800-17141800	Active TSS	iPS-15b Cell Line	embryonic stem cell

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