Variant report

Variant	rs4985740
Chromosome Location	chr17:17084648-17084649
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17083452..17086510-chr17:17107054..17109094,3	K562	blood:
2	chr17:17084407..17085925-chr17:17138943..17141730,2	K562	blood:
3	chr17:17084528..17086994-chr17:17091747..17094642,2	K562	blood:

Variant related genes	Relation type
ENSG00000154803	Chromatin interaction
ENSG00000266498	Chromatin interaction
ENSG00000264187	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10852847	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11078374	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11867932	1.00[CHB][hapmap]
rs11867934	0.85[AMR][1000 genomes]
rs11871902	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs171394	1.00[CHB][hapmap]
rs1974721	0.82[AMR][1000 genomes]
rs2090018	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2271520	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2349646	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28461224	1.00[ASN][1000 genomes]
rs4247118	1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];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]
rs4985696	1.00[ASN][1000 genomes]
rs4985701	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4985702	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4985717	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];0.93[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7206981	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208973	1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7210879	0.82[AMR][1000 genomes]
rs7217091	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7220827	1.00[CHB][hapmap]
rs7221842	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7222311	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8064550	1.00[ASW][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8072184	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8073842	1.00[CHB][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs8079563	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9893911	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9898995	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9908767	1.00[ASN][1000 genomes]
rs9914671	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	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4985740	FLCN	cis	cerebellum	SCAN
rs4985740	FBXO48	trans	cerebellum	SCAN
rs4985740	UBB	cis	cerebellum	SCAN
rs4985740	TRPV2	cis	cerebellum	SCAN
rs4985740	TOM1L2	cis	cerebellum	SCAN
rs4985740	ULK2	cis	cerebellum	SCAN
rs4985740	LOC162632	cis	parietal	SCAN

Chromatin state (count:126 , 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	chr17:17030400-17089200	Strong transcription	Fetal Intestine Large	intestine
4	chr17:17038400-17093800	Strong transcription	Fetal Brain Female	brain
5	chr17:17045000-17088400	Strong transcription	Brain Germinal Matrix	brain
6	chr17:17045200-17093800	Strong transcription	Fetal Stomach	stomach
7	chr17:17051000-17093200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr17:17053200-17088200	Strong transcription	Gastric	stomach
9	chr17:17054800-17087000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr17:17055200-17089400	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr17:17055600-17092600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr17:17055800-17092600	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr17:17056000-17093600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr17:17056200-17088200	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr17:17056200-17092400	Strong transcription	Stomach Smooth Muscle	stomach
16	chr17:17056600-17093600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr17:17056800-17095000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr17:17059400-17089000	Strong transcription	A549	lung
19	chr17:17060400-17088200	Strong transcription	HSMM	muscle
20	chr17:17060400-17093400	Strong transcription	Liver	Liver
21	chr17:17060600-17088800	Strong transcription	Fetal Intestine Small	intestine
22	chr17:17060600-17089200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr17:17060800-17089000	Strong transcription	NHLF	lung
24	chr17:17060800-17089400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr17:17060800-17093600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr17:17061400-17085200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr17:17061400-17089000	Strong transcription	Osteobl	bone
28	chr17:17061400-17090200	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr17:17062800-17085400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr17:17067800-17092200	Strong transcription	Brain Cingulate Gyrus	brain
31	chr17:17071800-17087800	Strong transcription	NH-A	brain
32	chr17:17073800-17088000	Strong transcription	NHDF-Ad	bronchial
33	chr17:17074000-17088200	Strong transcription	Pancreas	Pancrea
34	chr17:17074000-17088400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr17:17074400-17085200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr17:17074800-17087600	Strong transcription	HSMMtube	muscle
37	chr17:17075200-17087600	Strong transcription	Colon Smooth Muscle	Colon
38	chr17:17075200-17087800	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr17:17075200-17087800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr17:17075200-17088200	Strong transcription	Ovary	ovary
41	chr17:17075200-17089000	Strong transcription	Brain Angular Gyrus	brain
42	chr17:17075400-17086400	Strong transcription	Brain Substantia Nigra	brain
43	chr17:17075400-17086600	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr17:17075400-17087600	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr17:17075600-17085600	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr17:17075600-17087000	Strong transcription	Lung	lung
47	chr17:17076000-17084800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr17:17076000-17086400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr17:17076000-17087600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr17:17076000-17087800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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