Variant report

Variant	rs1242485
Chromosome Location	chr17:17349495-17349496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17344606..17346836-chr17:17348575..17350374,2	K562	blood:
2	chr17:17289655..17293959-chr17:17349314..17352438,5	MCF-7	breast:
3	chr17:17347836..17349791-chr17:17356884..17358605,2	MCF-7	breast:
4	chr17:17348389..17350727-chr17:17740115..17741953,2	MCF-7	breast:
5	chr17:17260627..17264124-chr17:17347628..17351557,3	MCF-7	breast:
6	chr17:17341170..17345071-chr17:17347034..17351413,6	MCF-7	breast:
7	chr17:17348329..17350736-chr18:19191275..19193632,2	MCF-7	breast:
8	chr17:17345336..17348353-chr17:17348575..17352300,3	K562	blood:
9	chr17:17347625..17349777-chr17:17725439..17727969,2	MCF-7	breast:
10	chr17:17265082..17270324-chr17:17346925..17351276,6	MCF-7	breast:
11	chr17:17344282..17356772-chr17:17394630..17405312,31	MCF-7	breast:
12	chr17:17342531..17346072-chr17:17347773..17351460,6	MCF-7	breast:
13	chr17:17347048..17349813-chr17:17378788..17383911,5	MCF-7	breast:
14	chr17:17349350..17351226-chr17:17382738..17384846,2	K562	blood:
15	chr17:17319589..17321575-chr17:17348151..17350364,2	MCF-7	breast:
16	chr17:17335195..17342131-chr17:17347291..17351486,7	MCF-7	breast:
17	chr17:17346012..17348708-chr17:17349032..17351296,2	MCF-7	breast:
18	chr17:17264792..17266427-chr17:17348267..17350277,2	MCF-7	breast:
19	chr17:17257302..17260550-chr17:17346867..17350783,4	MCF-7	breast:
20	chr17:17348675..17350534-chr17:17351603..17353201,2	MCF-7	breast:
21	chr17:17340093..17354118-chr17:17394085..17402192,31	MCF-7	breast:
22	chr17:17349182..17349868-chr17:17399782..17400771,2	MCF-7	breast:
23	chr17:17347016..17350522-chr17:17380134..17385375,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000108551	Chromatin interaction
ENSG00000072310	Chromatin interaction
ENSG00000141026	Chromatin interaction
ENSG00000167088	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1242477	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1242478	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1242479	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1242480	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1242481	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1242482	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1242486	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1242487	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1242488	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1242509	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16961730	0.86[CEU][hapmap]
rs2694924	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482648	chr17:17315268-17455442	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1065710	chr17:17328111-17391443	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv907729	chr17:17338536-17425279	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17330200-17350000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr17:17344000-17350000	Weak transcription	Dnd41	blood
3	chr17:17344800-17353400	Weak transcription	Brain Germinal Matrix	brain
4	chr17:17346800-17352200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr17:17347200-17350000	Weak transcription	Thymus	Thymus
6	chr17:17348200-17350400	Enhancers	Spleen	Spleen
7	chr17:17348200-17350400	Flanking Active TSS	Hela-S3	cervix
8	chr17:17348200-17351000	Flanking Active TSS	HepG2	liver
9	chr17:17348200-17351400	Enhancers	Adipose Nuclei	Adipose
10	chr17:17348200-17351400	Enhancers	Fetal Thymus	thymus
11	chr17:17348200-17351800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr17:17348400-17349600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr17:17348400-17349600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr17:17348400-17349800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr17:17348400-17350200	Enhancers	NHLF	lung
16	chr17:17348400-17350600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr17:17348400-17351600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr17:17348400-17352000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr17:17348600-17349600	Enhancers	H1 Cell Line	embryonic stem cell
20	chr17:17348600-17349600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr17:17348600-17349800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
22	chr17:17348600-17350000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr17:17348600-17350000	Enhancers	Fetal Muscle Trunk	muscle
24	chr17:17348600-17350200	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr17:17348600-17350200	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr17:17348600-17350400	Enhancers	Fetal Muscle Leg	muscle
27	chr17:17348600-17350400	Enhancers	Gastric	stomach
28	chr17:17348600-17350400	Flanking Active TSS	A549	lung
29	chr17:17348600-17351600	Enhancers	NH-A	brain
30	chr17:17348800-17349600	Enhancers	H9 Cell Line	embryonic stem cell
31	chr17:17348800-17349600	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr17:17348800-17350000	Enhancers	Fetal Heart	heart
33	chr17:17348800-17350200	Enhancers	HSMMtube	muscle
34	chr17:17348800-17350400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr17:17348800-17350400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr17:17348800-17350400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr17:17348800-17350600	Enhancers	Stomach Mucosa	stomach
38	chr17:17348800-17350600	Enhancers	NHDF-Ad	bronchial
39	chr17:17348800-17351000	Enhancers	Lung	lung
40	chr17:17348800-17351400	Enhancers	Liver	Liver
41	chr17:17349000-17349600	Enhancers	Left Ventricle	heart
42	chr17:17349000-17349600	Enhancers	Right Atrium	heart
43	chr17:17349000-17349600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr17:17349000-17349600	Enhancers	HMEC	breast
45	chr17:17349000-17349600	Flanking Active TSS	Osteobl	bone
46	chr17:17349000-17350200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr17:17349200-17349600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr17:17349200-17349600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
49	chr17:17349200-17349600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr17:17349200-17349600	Flanking Active TSS	HSMM	muscle

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