Variant report

Variant	rs6502570
Chromosome Location	chr17:17183255-17183256
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:17183193-17183813	HepG2	liver:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17177648..17180936-chr17:17181197..17184729,6	MCF-7	breast:
2	chr17:17182421..17186483-chr17:17204152..17209830,5	MCF-7	breast:
3	chr17:17138280..17141930-chr17:17183181..17187644,4	MCF-7	breast:
4	chr17:17139508..17142367-chr17:17182538..17186121,3	MCF-7	breast:
5	chr17:17138181..17140588-chr17:17182569..17184810,2	K562	blood:
6	chr17:17183059..17186537-chr17:17204352..17209458,5	K562	blood:
7	chr17:17086210..17088657-chr17:17181524..17183953,3	K562	blood:
8	chr17:17108079..17111792-chr17:17180254..17184300,4	K562	blood:
9	chr17:17109460..17111792-chr17:17182647..17184300,2	K562	blood:
10	chr17:17181690..17186423-chr17:17204352..17210529,13	K562	blood:
11	chr17:17173847..17176636-chr17:17182577..17185189,4	MCF-7	breast:
12	chr17:17175034..17177881-chr17:17182376..17183909,2	K562	blood:

No data

Variant related genes	Relation type
COPS3	TF binding region
ENSG00000154803	Chromatin interaction
ENSG00000141030	Chromatin interaction
ENSG00000264187	Chromatin interaction
ENSG00000205309	Chromatin interaction
ENSG00000266498	Chromatin interaction
ENSG00000179598	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12453455	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12600589	0.90[ASN][1000 genomes]
rs1630656	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1708617	0.92[ASN][1000 genomes]
rs1708621	0.92[ASN][1000 genomes]
rs1708624	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1708625	0.82[EUR][1000 genomes]
rs1708628	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1736204	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1736205	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1736208	0.94[ASN][1000 genomes]
rs1736209	0.94[ASN][1000 genomes]
rs1736211	0.92[ASN][1000 genomes]
rs1736212	0.92[ASN][1000 genomes]
rs1736216	0.92[ASN][1000 genomes]
rs1736217	0.92[ASN][1000 genomes]
rs1736221	0.90[ASN][1000 genomes]
rs2012954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2018781	0.92[ASN][1000 genomes]
rs2292527	0.88[ASN][1000 genomes]
rs2472689	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36079048	0.88[ASN][1000 genomes]
rs3866959	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4985760	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62066065	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62066066	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6502564	0.80[ASN][1000 genomes]
rs6502568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502571	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7217560	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7220577	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7220827	0.86[EUR][1000 genomes]
rs7221553	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224598	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7225876	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8066090	0.92[ASN][1000 genomes]
rs8080386	0.90[ASN][1000 genomes]
rs9892352	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9894565	0.92[ASN][1000 genomes]

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	nsv9499	chr17:17181611-17187670	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17174600-17183400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:17179000-17183600	Weak transcription	Aorta	Aorta
3	chr17:17180600-17183400	Weak transcription	Ovary	ovary
4	chr17:17182000-17183400	Enhancers	Primary B cells from peripheral blood	blood
5	chr17:17182400-17183600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr17:17182400-17183600	Enhancers	Stomach Mucosa	stomach
7	chr17:17182400-17183800	Enhancers	Fetal Brain Male	brain
8	chr17:17182600-17183400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr17:17182600-17183400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
10	chr17:17182600-17183400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr17:17182600-17183400	Enhancers	Brain Substantia Nigra	brain
12	chr17:17182600-17183400	Enhancers	Placenta	Placenta
13	chr17:17182600-17183400	Flanking Active TSS	Rectal Smooth Muscle	rectum
14	chr17:17182600-17183600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr17:17182600-17183600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr17:17182600-17183600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr17:17182600-17183800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr17:17182600-17184000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr17:17182800-17183400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr17:17182800-17183400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr17:17182800-17183400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr17:17182800-17183400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr17:17182800-17183400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr17:17182800-17183400	Flanking Active TSS	Brain Anterior Caudate	brain
25	chr17:17182800-17183400	Flanking Active TSS	Brain Hippocampus Middle	brain
26	chr17:17182800-17183400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
27	chr17:17182800-17183400	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr17:17182800-17183400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr17:17182800-17183400	Flanking Active TSS	GM12878-XiMat	blood
30	chr17:17182800-17183400	Flanking Active TSS	Hela-S3	cervix
31	chr17:17182800-17183400	Flanking Active TSS	HepG2	liver
32	chr17:17182800-17183400	Flanking Active TSS	HMEC	breast
33	chr17:17182800-17183400	Flanking Active TSS	NH-A	brain
34	chr17:17182800-17183400	Flanking Active TSS	NHLF	lung
35	chr17:17182800-17183600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr17:17182800-17183600	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr17:17182800-17183600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr17:17182800-17183600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr17:17182800-17183600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr17:17182800-17183600	Flanking Active TSS	Fetal Brain Female	brain
41	chr17:17182800-17183600	Flanking Active TSS	Fetal Intestine Small	intestine
42	chr17:17182800-17183600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr17:17182800-17183600	Flanking Active TSS	HUVEC	blood vessel
44	chr17:17182800-17183600	Flanking Active TSS	Osteobl	bone
45	chr17:17182800-17183800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr17:17182800-17185000	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr17:17182800-17185000	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr17:17183000-17183400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr17:17183000-17183400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr17:17183000-17183400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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