Variant report

Variant	rs1047799
Chromosome Location	chr17:17095487-17095488
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17089905..17092856-chr17:17094714..17097551,4	K562	blood:
2	chr17:17092917..17095538-chr17:17100650..17103433,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C17orf84-1	chr17:17091982-17095962	ENSG00000259850.1
2	lnc-C17orf84-1	chr17:17093701-17095957	NONHSAT146066

Extended variants
information (count: 66 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1047805	0.95[ASN][1000 genomes]
rs10852846	0.89[ASN][1000 genomes]
rs11078371	0.94[CHB][hapmap];1.00[CHD][hapmap]
rs11078373	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1110505	0.92[ASN][1000 genomes]
rs11551189	0.91[ASN][1000 genomes]
rs11651938	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11652678	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11654887	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11657189	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11870035	0.90[ASN][1000 genomes]
rs11870483	0.80[ASN][1000 genomes]
rs12601422	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs12602583	0.95[ASN][1000 genomes]
rs12602592	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1567815	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17794784	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2292526	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2292530	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2349645	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2349648	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28452405	0.82[AMR][1000 genomes]
rs34001712	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34976658	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3744125	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3744127	0.95[ASN][1000 genomes]
rs3744131	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3744132	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3744134	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3744136	0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3744137	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs3744138	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs3744139	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3826305	0.94[ASN][1000 genomes]
rs4073688	0.83[CHB][hapmap];0.97[CHD][hapmap]
rs4074612	0.94[CHB][hapmap]
rs4074819	0.87[ASN][1000 genomes]
rs4283273	0.95[ASN][1000 genomes]
rs4321246	0.87[ASN][1000 genomes]
rs4468683	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4629023	0.94[CHB][hapmap];1.00[CHD][hapmap]
rs4985703	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4985704	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4985730	0.80[ASN][1000 genomes]
rs4985737	0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4985741	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4985742	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4985743	0.94[ASN][1000 genomes]
rs4985745	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56133536	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58326998	0.89[ASN][1000 genomes]
rs59394251	0.89[ASN][1000 genomes]
rs7211576	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7214429	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs7216677	0.87[ASN][1000 genomes]
rs7218781	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs8066111	0.84[ASN][1000 genomes]
rs8066234	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8069259	0.87[ASN][1000 genomes]
rs8077360	0.87[ASN][1000 genomes]
rs9893676	0.91[ASN][1000 genomes]
rs9895060	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9897510	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9910857	0.93[EUR][1000 genomes];0.90[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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1047799	TOM1L2	cis	cerebellum	SCAN
rs1047799	PLD6	cis	parietal	SCAN
rs1047799	FLCN	cis	cerebellum	SCAN
rs1047799	ZNF624	cis	parietal	SCAN
rs1047799	FLCN	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17076600-17104600	Weak transcription	K562	blood
2	chr17:17086400-17104800	Weak transcription	Brain Substantia Nigra	brain
3	chr17:17086400-17106600	Weak transcription	Colonic Mucosa	Colon
4	chr17:17089600-17096600	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr17:17090200-17107000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr17:17090200-17107400	Weak transcription	Small Intestine	intestine
7	chr17:17090600-17095600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr17:17090800-17106600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr17:17090800-17106600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr17:17090800-17107200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr17:17091200-17104400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr17:17091400-17104000	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr17:17091800-17107600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr17:17092200-17105400	Weak transcription	Gastric	stomach
15	chr17:17092400-17104200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr17:17092400-17105600	Weak transcription	Brain Germinal Matrix	brain
17	chr17:17092800-17095600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr17:17092800-17096200	Enhancers	Colon Smooth Muscle	Colon
19	chr17:17093000-17095600	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr17:17093000-17104800	Weak transcription	Hela-S3	cervix
21	chr17:17093200-17095600	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr17:17093200-17095600	Enhancers	Left Ventricle	heart
23	chr17:17093200-17095600	Genic enhancers	A549	lung
24	chr17:17093200-17095600	Enhancers	NH-A	brain
25	chr17:17093200-17095800	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr17:17093400-17095600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr17:17093400-17095600	Enhancers	Stomach Smooth Muscle	stomach
28	chr17:17093400-17096200	Enhancers	NHLF	lung
29	chr17:17093600-17095600	Enhancers	NHDF-Ad	bronchial
30	chr17:17093600-17102400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr17:17093600-17103400	Weak transcription	Fetal Thymus	thymus
32	chr17:17093600-17104400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr17:17093600-17107400	Weak transcription	Dnd41	blood
34	chr17:17093600-17108400	Weak transcription	Thymus	Thymus
35	chr17:17093800-17095600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr17:17093800-17095600	Enhancers	Adipose Nuclei	Adipose
37	chr17:17093800-17095600	Enhancers	Placenta	Placenta
38	chr17:17093800-17095600	Strong transcription	HMEC	breast
39	chr17:17093800-17095600	Enhancers	Osteobl	bone
40	chr17:17093800-17096600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr17:17093800-17096600	Enhancers	Brain Anterior Caudate	brain
42	chr17:17093800-17097200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr17:17093800-17103400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr17:17093800-17104000	Weak transcription	Fetal Intestine Small	intestine
45	chr17:17093800-17104200	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr17:17093800-17105400	Weak transcription	Pancreas	Pancrea
47	chr17:17093800-17105600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr17:17093800-17105600	Weak transcription	Esophagus	oesophagus
49	chr17:17093800-17107400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr17:17093800-17107600	Weak transcription	Monocytes-CD14+_RO01746	blood

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