Variant report

Variant	rs17098297
Chromosome Location	chr1:78215392-78215393
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:78215280-78215411	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr1:78215307-78215417	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:78215199-78215687	K562	blood:	n/a	n/a
4	FOS	chr1:78215182-78215408	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:78213598..78216236-chr1:78219980..78222063,2	K562	blood:
2	chr1:78215243..78217892-chr1:78468395..78470149,2	K562	blood:
3	chr1:78213808..78218227-chr1:78468436..78472020,4	K562	blood:
4	chr1:78212750..78216522-chr1:78224934..78227358,4	MCF-7	breast:
5	chr1:78214828..78217072-chr1:78230959..78232722,2	K562	blood:

Variant related genes	Relation type
USP33	TF binding region
ENSG00000077254	Chromatin interaction
ENSG00000162616	Chromatin interaction
ENSG00000273338	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12027183	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12027952	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12030080	0.82[JPT][hapmap]
rs12035132	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17100944	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41292270	0.85[AMR][1000 genomes]
rs56861428	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58022842	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59656850	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7525039	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9728416	1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv830303	chr1:78090824-78308765	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
5	esv1796958	chr1:78138955-78267421	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv1798160	chr1:78149941-78267421	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
8	nsv508326	chr1:78184379-78234247	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1004327	chr1:78212804-78352385	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78173800-78224400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:78191600-78215600	Weak transcription	A549	lung
3	chr1:78192200-78222400	Weak transcription	Brain Substantia Nigra	brain
4	chr1:78193000-78221200	Weak transcription	Brain Angular Gyrus	brain
5	chr1:78193600-78222600	Weak transcription	Fetal Kidney	kidney
6	chr1:78194400-78223400	Weak transcription	NH-A	brain
7	chr1:78195400-78216000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:78195400-78216800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:78195400-78222200	Weak transcription	Gastric	stomach
10	chr1:78195400-78223200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:78195400-78224200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:78195400-78224800	Weak transcription	Spleen	Spleen
13	chr1:78196800-78221800	Weak transcription	Ovary	ovary
14	chr1:78197800-78221800	Weak transcription	Thymus	Thymus
15	chr1:78197800-78222400	Weak transcription	Fetal Intestine Small	intestine
16	chr1:78197800-78223400	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:78198200-78222200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:78198400-78224000	Weak transcription	Esophagus	oesophagus
19	chr1:78200200-78218800	Weak transcription	HUVEC	blood vessel
20	chr1:78202800-78217000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:78205400-78220200	Weak transcription	GM12878-XiMat	blood
22	chr1:78205400-78221800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:78205600-78222200	Weak transcription	Fetal Brain Male	brain
24	chr1:78206000-78216000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:78206000-78216800	Weak transcription	Primary T cells from cord blood	blood
26	chr1:78206000-78222000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr1:78206000-78222200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:78206000-78224400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:78206400-78222000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:78206400-78222400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:78206400-78224000	Weak transcription	Fetal Intestine Large	intestine
32	chr1:78206400-78224000	Weak transcription	HSMM	muscle
33	chr1:78206600-78215800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:78206600-78220200	Weak transcription	Dnd41	blood
35	chr1:78206600-78220800	Weak transcription	Hela-S3	cervix
36	chr1:78206600-78221000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:78206600-78221200	Weak transcription	Fetal Thymus	thymus
38	chr1:78206600-78221400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:78206600-78221600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:78206600-78222000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:78206600-78222000	Weak transcription	Primary B cells from cord blood	blood
42	chr1:78206600-78222200	Weak transcription	Brain Germinal Matrix	brain
43	chr1:78206600-78222400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr1:78206600-78223200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr1:78206600-78223200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:78206600-78223400	Weak transcription	Primary B cells from peripheral blood	blood
47	chr1:78206600-78224000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:78206800-78215800	Weak transcription	Placenta	Placenta
49	chr1:78206800-78216800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:78206800-78223400	Weak transcription	Fetal Brain Female	brain

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