Variant report

Variant	rs17509390
Chromosome Location	chr1:114353324-114353325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr1:114353147-114355793	SK-N-SH	brain:	n/a	n/a
2	EGR1	chr1:114353034-114356186	MCF-7	breast:	n/a	n/a
3	POLR2A	chr1:114353126-114355605	MCF10A-Er-Src	breast:	n/a	n/a
4	SIN3AK20	chr1:114353302-114355963	MCF-7	breast:	n/a	n/a
5	CEBPB	chr1:114353039-114353378	Hela-S3	cervix:	n/a	chr1:114353199-114353210 chr1:114353198-114353209
6	KAP1	chr1:114353138-114353557	K562	blood:	n/a	n/a
7	CEBPB	chr1:114353095-114353333	K562	blood:	n/a	chr1:114353199-114353210 chr1:114353198-114353209
8	MXI1	chr1:114353169-114355409	Hela-S3	cervix:	n/a	n/a
9	CEBPB	chr1:114353067-114353335	HepG2	liver:	n/a	chr1:114353199-114353210 chr1:114353198-114353209
10	JUN	chr1:114352049-114356471	K562	blood:	n/a	n/a

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114327966..114331682-chr1:114351317..114354646,4	K562	blood:
2	chr1:114324677..114327047-chr1:114352445..114354886,5	MCF-7	breast:
3	chr1:114351776..114354778-chr1:114417690..114420488,3	MCF-7	breast:
4	chr1:114352745..114355342-chr1:114397110..114401660,4	MCF-7	breast:
5	chr1:114351760..114356326-chr1:114471041..114474785,9	K562	blood:
6	chr1:114352914..114355173-chr8:67972851..67974547,2	MCF-7	breast:
7	chr1:114352160..114355349-chr1:114470537..114474785,4	K562	blood:
8	chr1:114353271..114354789-chr1:114442800..114445051,2	MCF-7	breast:
9	chr1:114352306..114358140-chr1:114445806..114450844,18	MCF-7	breast:
10	chr1:114299192..114304079-chr1:114351100..114353758,4	K562	blood:
11	chr1:108226178..108228590-chr1:114353094..114356101,3	MCF-7	breast:
12	chr1:108269564..108272129-chr1:114352003..114353705,2	MCF-7	breast:
13	chr1:114353074..114355128-chr9:133814434..133817147,2	MCF-7	breast:
14	chr1:114307008..114312126-chr1:114352475..114355930,7	MCF-7	breast:
15	chr1:108229330..108231475-chr1:114352461..114355425,3	MCF-7	breast:
16	chr1:114353249..114355008-chr17:59488182..59490622,2	MCF-7	breast:
17	chr1:114353086..114356383-chr1:114467552..114475359,15	MCF-7	breast:
18	chr1:114353164..114356409-chr1:114439569..114442509,4	MCF-7	breast:
19	chr1:114352137..114357235-chr1:114445065..114452395,18	MCF-7	breast:
20	chr1:114352766..114354968-chr1:114504894..114507135,2	MCF-7	breast:
21	chr1:114300040..114303354-chr1:114351974..114356702,9	MCF-7	breast:
22	chr1:114353223..114356831-chr1:115298921..115302043,5	MCF-7	breast:
23	chr1:114352743..114357488-chr1:114365626..114369516,6	MCF-7	breast:
24	chr1:114298167..114305255-chr1:114351008..114356451,27	MCF-7	breast:
25	chr1:114353109..114354990-chr1:114522325..114525289,2	MCF-7	breast:
26	chr1:108291627..108293246-chr1:114353081..114355950,2	MCF-7	breast:
27	chr1:114352067..114356642-chr1:114470131..114477025,16	MCF-7	breast:
28	chr1:114352670..114354884-chr1:114372315..114375244,2	K562	blood:
29	chr1:114351754..114354517-chr1:115321851..115324314,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000231128	TF binding region
ENSG00000187013	Chromatin interaction
ENSG00000116793	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000130720	Chromatin interaction
ENSG00000116774	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000052723	Chromatin interaction
ENSG00000235527	Chromatin interaction
ENSG00000226167	Chromatin interaction
ENSG00000121022	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000134262	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000081019	Chromatin interaction
ENSG00000134215	Chromatin interaction
ENSG00000009307	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10127930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10489936	0.87[EUR][1000 genomes]
rs1080307	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1217384	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12723023	0.82[EUR][1000 genomes]
rs12729708	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12730735	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12731010	0.85[EUR][1000 genomes]
rs12734625	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12735104	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739970	0.82[EUR][1000 genomes]
rs12746609	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12748727	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12752932	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12753075	0.84[EUR][1000 genomes]
rs12753351	0.87[EUR][1000 genomes]
rs12758546	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12760457	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13374352	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17274550	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17274620	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17274634	0.88[EUR][1000 genomes]
rs17359302	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17462614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1885454	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2040040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2359173	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2359174	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34042871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34341173	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34649199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34698891	0.89[EUR][1000 genomes]
rs34857922	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34877889	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35320278	0.88[EUR][1000 genomes]
rs35383900	0.87[EUR][1000 genomes]
rs35836713	0.88[EUR][1000 genomes]
rs36115604	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3747998	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3748003	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3761931	0.87[EUR][1000 genomes]
rs3789595	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3789599	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3789607	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789609	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61817579	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61817586	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61817617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61819423	0.84[EUR][1000 genomes]
rs61819424	0.81[EUR][1000 genomes]
rs61820162	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6668829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6674848	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6703387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71662845	0.80[EUR][1000 genomes]
rs7533391	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7533605	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7549685	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7555354	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9803891	0.85[EUR][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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114303400-114353800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:114309600-114353400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:114320000-114354000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:114329200-114353600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:114332400-114353400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:114340600-114353400	Weak transcription	Fetal Muscle Leg	muscle
7	chr1:114348200-114353600	Weak transcription	Placenta	Placenta
8	chr1:114348600-114353800	Weak transcription	Gastric	stomach
9	chr1:114349800-114353600	Weak transcription	Lung	lung
10	chr1:114350800-114353400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:114351000-114353600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr1:114351400-114353400	Enhancers	Brain Substantia Nigra	brain
13	chr1:114351400-114354000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:114351600-114353400	Flanking Active TSS	Dnd41	blood
15	chr1:114351600-114353600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:114351600-114353600	Enhancers	Fetal Heart	heart
17	chr1:114351600-114353800	Weak transcription	Pancreas	Pancrea
18	chr1:114351800-114353400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:114351800-114353600	Enhancers	Primary B cells from peripheral blood	blood
20	chr1:114351800-114355400	Active TSS	NHLF	lung
21	chr1:114351800-114355600	Active TSS	Psoas Muscle	Psoas
22	chr1:114352000-114353400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr1:114352000-114353600	Weak transcription	Stomach Mucosa	stomach
24	chr1:114352000-114353600	Active TSS	Stomach Smooth Muscle	stomach
25	chr1:114352000-114353800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:114352000-114354400	Active TSS	Right Atrium	heart
27	chr1:114352000-114355800	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr1:114352000-114355800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:114352200-114353400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr1:114352200-114355400	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr1:114352200-114355400	Active TSS	GM12878-XiMat	blood
32	chr1:114352200-114355400	Active TSS	Hela-S3	cervix
33	chr1:114352200-114355800	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr1:114352400-114353600	Flanking Active TSS	HUVEC	blood vessel
35	chr1:114352400-114354200	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr1:114352400-114354200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:114352400-114354400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr1:114352400-114355200	Active TSS	Primary T cells fromperipheralblood	blood
39	chr1:114352400-114355400	Active TSS	Fetal Intestine Large	intestine
40	chr1:114352400-114355400	Active TSS	Fetal Thymus	thymus
41	chr1:114352400-114355800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:114352400-114356200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:114352600-114353400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:114352600-114353400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:114352600-114353400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr1:114352600-114353400	Enhancers	Small Intestine	intestine
47	chr1:114352600-114353400	Flanking Active TSS	Osteobl	bone
48	chr1:114352600-114354000	Flanking Active TSS	Liver	Liver
49	chr1:114352600-114354200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr1:114352600-114354400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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