Variant report

Variant	rs2597169
Chromosome Location	chr17:46034091-46034092
allele	A/G
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:46004717..46007682-chr17:46032533..46035119,2	K562	blood:
2	chr17:46033378..46035935-chr17:46129952..46132940,2	MCF-7	breast:
3	chr17:45925187..45928793-chr17:46033650..46037470,3	MCF-7	breast:
4	chr17:45917897..45920844-chr17:46033567..46035986,3	MCF-7	breast:
5	chr17:46032611..46035777-chr17:46183682..46186625,3	MCF-7	breast:
6	chr17:46033549..46039001-chr17:46046732..46050276,6	K562	blood:
7	chr17:46033818..46036436-chr17:48943075..48944680,2	MCF-7	breast:
8	chr17:45898563..45901614-chr17:46033321..46036165,3	MCF-7	breast:
9	chr17:46033611..46036450-chr20:45980908..45983000,2	MCF-7	breast:
10	chr17:46031321..46037809-chr17:46043555..46050276,13	K562	blood:
11	chr17:45969751..45975935-chr17:46032072..46038613,14	MCF-7	breast:
12	chr17:45917528..45920214-chr17:46032690..46035678,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000229980	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000006025	Chromatin interaction
ENSG00000141232	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000231119	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000141295	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11079802	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1130932	0.80[MEX][hapmap]
rs11651753	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs16949418	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs16949720	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2002136	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2318118	0.80[MEX][hapmap]
rs2325748	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2428608	0.92[ASN][1000 genomes]
rs2525095	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2525109	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.86[MKK][hapmap];0.86[YRI][hapmap];0.97[ASN][1000 genomes]
rs2525110	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.97[ASN][1000 genomes]
rs2875735	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764396	0.80[MEX][hapmap]
rs3764398	0.89[ASN][1000 genomes]
rs3826396	0.97[ASN][1000 genomes]
rs4793738	0.99[ASN][1000 genomes]
rs4794331	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs57768342	0.95[ASN][1000 genomes]
rs61665404	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6503934	0.80[MEX][hapmap]
rs7207225	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs7220104	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs72823505	0.96[ASN][1000 genomes]
rs9895863	0.80[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2597169	NFE2L1	cis	cerebellum	SCAN
rs2597169	SP2	cis	lymphoblastoid	seeQTL
rs2597169	ETV4	cis	cerebellum	SCAN
rs2597169	PNPO	cis	Nerve Tibial	GTEx
rs2597169	CALCOCO2	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019800-46034200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
3	chr17:46020000-46034600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr17:46027200-46034400	Weak transcription	Hela-S3	cervix
5	chr17:46027200-46047200	Weak transcription	Spleen	Spleen
6	chr17:46027400-46034200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr17:46027400-46034400	Weak transcription	Fetal Lung	lung
8	chr17:46027400-46034600	Weak transcription	K562	blood
9	chr17:46027400-46034800	Weak transcription	NH-A	brain
10	chr17:46027600-46034200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr17:46027600-46034400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr17:46027600-46034800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr17:46027600-46047400	Weak transcription	Right Ventricle	heart
14	chr17:46027600-46047600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr17:46027800-46034200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr17:46028000-46047400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr17:46028000-46047600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr17:46029200-46035200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
19	chr17:46029600-46034600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr17:46029800-46034200	Weak transcription	Brain Anterior Caudate	brain
21	chr17:46030000-46035000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr17:46030200-46034400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr17:46030200-46045800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr17:46030400-46034200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr17:46030400-46035200	Weak transcription	Osteobl	bone
26	chr17:46030600-46035600	Active TSS	Colonic Mucosa	Colon
27	chr17:46031200-46034200	Active TSS	Fetal Stomach	stomach
28	chr17:46031200-46035200	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr17:46031400-46034600	Weak transcription	NHEK	skin
30	chr17:46031400-46035600	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr17:46031400-46036000	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr17:46031400-46039000	Weak transcription	Primary T cells from cord blood	blood
33	chr17:46031800-46034400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr17:46032000-46037800	Active TSS	Rectal Smooth Muscle	rectum
35	chr17:46032200-46035400	Active TSS	Stomach Mucosa	stomach
36	chr17:46032200-46036200	Active TSS	Duodenum Mucosa	Duodenum
37	chr17:46032600-46034400	Enhancers	A549	lung
38	chr17:46032600-46035600	Enhancers	Liver	Liver
39	chr17:46032800-46035000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr17:46032800-46035200	Active TSS	Gastric	stomach
41	chr17:46032800-46035200	Active TSS	Small Intestine	intestine
42	chr17:46032800-46036400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr17:46032800-46037800	Enhancers	Fetal Thymus	thymus
44	chr17:46033000-46034400	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
45	chr17:46033000-46035200	Active TSS	Fetal Kidney	kidney
46	chr17:46033200-46034200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr17:46033200-46035200	Active TSS	Lung	lung
48	chr17:46033200-46035400	Active TSS	Fetal Intestine Large	intestine
49	chr17:46033200-46035400	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr17:46033400-46034200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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