Variant report

Variant	rs4985696
Chromosome Location	chr17:17003436-17003437
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17001973..17004582-chr17:17006426..17009352,2	MCF-7	breast:
2	chr17:17000263..17003828-chr17:17006059..17008926,3	MCF-7	breast:
3	chr17:16996588..16998552-chr17:17003380..17006242,3	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10852847	1.00[CHB][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078374	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078376	0.81[AFR][1000 genomes]
rs11656868	1.00[CHB][hapmap]
rs11871902	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1974721	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2090018	1.00[ASN][1000 genomes]
rs2271520	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2349646	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28461224	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4247118	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4247120	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4275914	1.00[ASN][1000 genomes]
rs4514740	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4985701	1.00[ASN][1000 genomes]
rs4985702	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4985717	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985740	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4985746	1.00[ASN][1000 genomes]
rs4985778	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6502563	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7206981	1.00[ASN][1000 genomes]
rs7207485	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7208929	1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7208973	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7217091	1.00[CHB][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs7220827	1.00[CHB][hapmap]
rs7221842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7222311	1.00[ASN][1000 genomes]
rs8064550	1.00[ASN][1000 genomes]
rs8072184	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8073842	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8079563	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9893911	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9898995	1.00[ASN][1000 genomes]
rs9908767	1.00[ASN][1000 genomes]
rs9914671	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4985696	FLCN	cis	cerebellum	SCAN
rs4985696	ULK2	cis	cerebellum	SCAN
rs4985696	TOM1L2	cis	cerebellum	SCAN
rs4985696	FBXO48	trans	cerebellum	SCAN
rs4985696	PLD6	cis	parietal	SCAN

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	chr17:16992400-17010000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr17:16993200-17003800	Genic enhancers	Fetal Intestine Small	intestine
4	chr17:16993400-17011400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr17:16994600-17011600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr17:16996400-17006200	Weak transcription	Liver	Liver
7	chr17:16997000-17016600	Enhancers	Left Ventricle	heart
8	chr17:16997200-17005000	Weak transcription	K562	blood
9	chr17:16997400-17006200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr17:16997400-17010000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr17:16998000-17003600	Genic enhancers	Fetal Stomach	stomach
12	chr17:16998200-17016200	Enhancers	Fetal Heart	heart
13	chr17:16998600-17003800	Enhancers	Right Atrium	heart
14	chr17:16998600-17004000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr17:16998600-17006800	Enhancers	Psoas Muscle	Psoas
16	chr17:16998600-17015400	Genic enhancers	Fetal Muscle Leg	muscle
17	chr17:16998600-17016600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr17:16999000-17012800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr17:16999200-17006400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr17:16999600-17003600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr17:16999600-17005000	Weak transcription	Gastric	stomach
22	chr17:16999600-17008200	Strong transcription	Primary B cells from peripheral blood	blood
23	chr17:17000200-17005600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr17:17000200-17012600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr17:17000200-17018200	Weak transcription	NH-A	brain
26	chr17:17000400-17004000	Enhancers	Fetal Lung	lung
27	chr17:17000400-17005000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr17:17000600-17004000	Weak transcription	Primary T cells from cord blood	blood
29	chr17:17000600-17008000	Strong transcription	NHEK	skin
30	chr17:17000600-17009800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr17:17000600-17009800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr17:17001200-17004200	Weak transcription	Fetal Thymus	thymus
33	chr17:17001400-17007000	Weak transcription	Primary B cells from cord blood	blood
34	chr17:17001600-17003800	Genic enhancers	Fetal Intestine Large	intestine
35	chr17:17001600-17005600	Enhancers	Right Ventricle	heart
36	chr17:17001600-17010200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr17:17001600-17010800	Weak transcription	Aorta	Aorta
38	chr17:17001600-17011400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr17:17001800-17004400	Enhancers	Placenta	Placenta
40	chr17:17001800-17005600	Enhancers	Adipose Nuclei	Adipose
41	chr17:17001800-17006600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr17:17001800-17009200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr17:17001800-17009800	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr17:17001800-17012800	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr17:17002000-17003600	Weak transcription	Thymus	Thymus
46	chr17:17002000-17005600	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr17:17002000-17005800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr17:17002000-17006400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr17:17002000-17008400	Weak transcription	Hela-S3	cervix
50	chr17:17002000-17010200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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