Variant report

Variant	rs7220577
Chromosome Location	chr17:17149213-17149214
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17139773..17141689-chr17:17147238..17149246,2	MCF-7	breast:
2	chr17:17138850..17142014-chr17:17149192..17152269,3	K562	blood:
3	chr17:17146996..17149508-chr17:17150450..17152248,2	K562	blood:
4	chr17:17147939..17150281-chr17:17183069..17185627,2	K562	blood:
5	chr17:17139635..17142575-chr17:17144486..17149716,4	K562	blood:

Variant related genes	Relation type
ENSG00000266498	Chromatin interaction
ENSG00000141030	Chromatin interaction
ENSG00000154803	Chromatin interaction
ENSG00000264187	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12453455	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12600589	0.92[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs12949822	0.81[ASN][1000 genomes]
rs1630656	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1708617	0.94[ASN][1000 genomes]
rs1708621	0.94[ASN][1000 genomes]
rs1708624	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1708625	0.83[EUR][1000 genomes]
rs1708628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1736204	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1736205	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1736208	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs1736209	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs1736211	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1736212	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1736216	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1736217	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.94[ASN][1000 genomes]
rs1736221	0.93[ASN][1000 genomes]
rs2012954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2018781	0.94[ASN][1000 genomes]
rs2292527	0.92[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2472689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36079048	0.90[ASN][1000 genomes]
rs3866959	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066065	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62066066	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6502564	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs6502568	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502569	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502570	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502571	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7217560	0.81[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs7220827	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs7221553	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7224598	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7225876	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066090	0.94[ASN][1000 genomes]
rs8080386	0.92[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs9892352	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9894565	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7220577	FLCN	cis	cerebellum	SCAN
rs7220577	TOM1L2	cis	cerebellum	SCAN
rs7220577	SMCR8	cis	cerebellum	SCAN
rs7220577	RAI1	cis	cerebellum	SCAN
rs7220577	FLCN	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17141400-17150400	Weak transcription	Aorta	Aorta
2	chr17:17141600-17149600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr17:17141600-17149800	Weak transcription	Esophagus	oesophagus
4	chr17:17141600-17149800	Weak transcription	Fetal Kidney	kidney
5	chr17:17141600-17150600	Weak transcription	Brain Angular Gyrus	brain
6	chr17:17141600-17161200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr17:17141800-17149400	Weak transcription	NHLF	lung
8	chr17:17141800-17149600	Weak transcription	Small Intestine	intestine
9	chr17:17141800-17149800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr17:17141800-17150000	Weak transcription	Primary T cells from cord blood	blood
11	chr17:17141800-17150000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr17:17141800-17150200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr17:17141800-17150200	Weak transcription	Fetal Lung	lung
14	chr17:17141800-17150200	Weak transcription	Pancreas	Pancrea
15	chr17:17141800-17150200	Weak transcription	HMEC	breast
16	chr17:17141800-17150200	Weak transcription	HSMM	muscle
17	chr17:17141800-17150400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr17:17141800-17150400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr17:17141800-17150800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr17:17141800-17155600	Weak transcription	Psoas Muscle	Psoas
21	chr17:17141800-17156600	Weak transcription	Fetal Heart	heart
22	chr17:17141800-17162200	Weak transcription	Stomach Mucosa	stomach
23	chr17:17142000-17149400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr17:17142000-17149400	Weak transcription	Placenta	Placenta
25	chr17:17142000-17149400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr17:17142000-17149400	Weak transcription	Thymus	Thymus
27	chr17:17142000-17149800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr17:17142000-17150200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr17:17142000-17150200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr17:17142000-17150200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr17:17142000-17150600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr17:17142000-17150600	Weak transcription	Hela-S3	cervix
33	chr17:17142000-17153200	Weak transcription	Fetal Brain Male	brain
34	chr17:17142200-17149600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr17:17142200-17149600	Weak transcription	Colon Smooth Muscle	Colon
36	chr17:17142200-17149800	Weak transcription	Gastric	stomach
37	chr17:17142200-17150200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr17:17142200-17151000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr17:17142400-17149400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr17:17143200-17150200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr17:17143400-17149400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr17:17143400-17150200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr17:17143800-17149800	Weak transcription	K562	blood
44	chr17:17146000-17171000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr17:17146200-17149800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr17:17146200-17149800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr17:17146200-17150400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr17:17146200-17150800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr17:17148400-17160000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr17:17148600-17159000	Strong transcription	Brain Hippocampus Middle	brain

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