Variant report

Variant	rs1708628
Chromosome Location	chr17:17147625-17147626
allele	C/T
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	chr17:17142608..17144134-chr17:17146092..17148091,2	K562	blood:
3	chr17:17146996..17149508-chr17:17150450..17152248,2	K562	blood:
4	chr17:17139354..17141733-chr17:17143268..17148053,6	MCF-7	breast:
5	chr17:17139635..17142575-chr17:17144486..17149716,4	K562	blood:

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

Extended variants
information (count: 41 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12453455	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12600589	0.92[CHB][hapmap]
rs12949822	0.85[AFR][1000 genomes]
rs1630656	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1708624	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1708625	0.84[EUR][1000 genomes]
rs1736204	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1736205	1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1736208	0.82[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1736209	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs1736211	0.82[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs1736212	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs1736216	1.00[CHB][hapmap];0.84[AMR][1000 genomes]
rs1736217	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.85[MEX][hapmap]
rs2012954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2292527	0.92[CHB][hapmap];0.96[CHD][hapmap]
rs2472689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3866959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4985760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62066065	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62066066	0.83[EUR][1000 genomes]
rs6502564	1.00[CHB][hapmap]
rs6502568	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6502569	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6502570	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6502571	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7217560	0.80[GIH][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes]
rs7220577	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]
rs7220827	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs7221553	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7224598	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7225876	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8080386	0.92[CHB][hapmap];0.96[CHD][hapmap]
rs9892352	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9894565	1.00[CHB][hapmap];0.93[CHD][hapmap]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1708628	COPS3	cis	multi-tissue	Pritchard
rs1708628	FLCN	cis	cerebellum	SCAN
rs1708628	TOM1L2	cis	cerebellum	SCAN
rs1708628	RAI1	cis	cerebellum	SCAN
rs1708628	FLCN	cis	parietal	SCAN
rs1708628	SMCR8	cis	cerebellum	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	chr17:17141600-17148600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr17:17141600-17149000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr17:17141600-17149000	Weak transcription	Fetal Brain Female	brain
5	chr17:17141600-17149000	Weak transcription	Left Ventricle	heart
6	chr17:17141600-17149000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr17:17141600-17149200	Weak transcription	Brain Substantia Nigra	brain
8	chr17:17141600-17149200	Weak transcription	Right Ventricle	heart
9	chr17:17141600-17149200	Weak transcription	Spleen	Spleen
10	chr17:17141600-17149200	Weak transcription	HSMMtube	muscle
11	chr17:17141600-17149600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr17:17141600-17149800	Weak transcription	Esophagus	oesophagus
13	chr17:17141600-17149800	Weak transcription	Fetal Kidney	kidney
14	chr17:17141600-17150600	Weak transcription	Brain Angular Gyrus	brain
15	chr17:17141600-17161200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr17:17141800-17148600	Weak transcription	Brain Hippocampus Middle	brain
17	chr17:17141800-17148600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr17:17141800-17148800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr17:17141800-17148800	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr17:17141800-17148800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr17:17141800-17148800	Weak transcription	Fetal Stomach	stomach
22	chr17:17141800-17148800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr17:17141800-17149000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr17:17141800-17149000	Weak transcription	Primary B cells from cord blood	blood
25	chr17:17141800-17149000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr17:17141800-17149000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr17:17141800-17149000	Weak transcription	Liver	Liver
28	chr17:17141800-17149000	Weak transcription	Brain Anterior Caudate	brain
29	chr17:17141800-17149000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr17:17141800-17149000	Weak transcription	Fetal Intestine Large	intestine
31	chr17:17141800-17149200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr17:17141800-17149200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr17:17141800-17149200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr17:17141800-17149200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr17:17141800-17149200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr17:17141800-17149200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr17:17141800-17149200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr17:17141800-17149200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr17:17141800-17149200	Weak transcription	NH-A	brain
40	chr17:17141800-17149200	Weak transcription	NHDF-Ad	bronchial
41	chr17:17141800-17149200	Weak transcription	NHEK	skin
42	chr17:17141800-17149400	Weak transcription	NHLF	lung
43	chr17:17141800-17149600	Weak transcription	Small Intestine	intestine
44	chr17:17141800-17149800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr17:17141800-17150000	Weak transcription	Primary T cells from cord blood	blood
46	chr17:17141800-17150000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr17:17141800-17150200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr17:17141800-17150200	Weak transcription	Fetal Lung	lung
49	chr17:17141800-17150200	Weak transcription	Pancreas	Pancrea
50	chr17:17141800-17150200	Weak transcription	HMEC	breast

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