Variant report

Variant	rs10919427
Chromosome Location	chr1:170507442-170507443
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	chr1:170506932-170507750	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr1:170507331-170507759	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr1:170507073-170507736	MCF10A-Er-Src	breast:	n/a	n/a
4	MEF2A	chr1:170507215-170507854	SK-N-SH	brain:	n/a	chr1:170507524-170507545 chr1:170507638-170507653 chr1:170507522-170507543 chr1:170507526-170507541 chr1:170507526-170507540 chr1:170507525-170507541 chr1:170507529-170507538 chr1:170507526-170507542 chr1:170507527-170507538 chr1:170507637-170507653 chr1:170507528-170507539 chr1:170507524-170507545
5	STAT3	chr1:170506930-170507744	MCF10A-Er-Src	breast:	n/a	n/a
6	TBP	chr1:170507419-170508587	GM12878	blood:	n/a	n/a
7	EBF1	chr1:170507341-170508864	GM12878	blood:	n/a	n/a
8	FOS	chr1:170507331-170507760	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr1:170507329-170507622	SK-N-SH	brain:	n/a	n/a
10	FOXA2	chr1:170507274-170507523	HepG2	liver:	n/a	n/a
11	ARID3A	chr1:170507206-170507659	HepG2	liver:	n/a	n/a
12	FOXA1	chr1:170506980-170507639	HepG2	liver:	n/a	n/a
13	RELA	chr1:170507398-170508781	GM12878	blood:	n/a	n/a
14	FOS	chr1:170507390-170507756	MCF10A-Er-Src	breast:	n/a	n/a
15	STAT3	chr1:170507259-170507647	MCF10A-Er-Src	breast:	n/a	n/a
16	MYC	chr1:170507390-170507661	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr1:170506799-170507825	GM12878	blood:	n/a	n/a
18	MEF2A	chr1:170507259-170507816	SK-N-SH	brain:	n/a	chr1:170507524-170507545 chr1:170507638-170507653 chr1:170507522-170507543 chr1:170507526-170507541 chr1:170507526-170507540 chr1:170507525-170507541 chr1:170507529-170507538 chr1:170507526-170507542 chr1:170507527-170507538 chr1:170507637-170507653 chr1:170507528-170507539 chr1:170507524-170507545
19	POLR2A	chr1:170507428-170507621	MCF10A-Er-Src	breast:	n/a	n/a
20	E2F4	chr1:170507295-170507646	MCF10A-Er-Src	breast:	n/a	n/a
21	FOS	chr1:170507365-170507743	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr1:170507424-170507681	MCF10A-Er-Src	breast:	n/a	n/a
23	MYC	chr1:170507426-170507736	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr1:170500588-170509342	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:170499484..170505100-chr1:170505427..170511134,13	MCF-7	breast:
2	chr1:170499494..170504219-chr1:170507198..170509728,4	K562	blood:
3	chr1:170505845..170507454-chr1:170512986..170515309,2	K562	blood:

Variant related genes	Relation type
GORAB	TF binding region
ENSG00000120370	Chromatin interaction
ENSG00000231407	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10919428	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12075840	0.89[AFR][1000 genomes]
rs12097444	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2901402	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59597526	0.95[AFR][1000 genomes]
rs60696673	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6676293	0.89[AFR][1000 genomes]
rs73029152	0.83[AFR][1000 genomes]
rs73029169	1.00[AMR][1000 genomes]

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	nsv872543	chr1:170171083-170674903	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv533915	chr1:170258766-170725296	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170501800-170516000	Weak transcription	Spleen	Spleen
2	chr1:170502000-170508400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:170502000-170515200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:170502000-170517200	Weak transcription	Esophagus	oesophagus
5	chr1:170502200-170508200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:170502200-170508400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:170502200-170508400	Weak transcription	Placenta	Placenta
8	chr1:170502200-170508400	Weak transcription	Fetal Thymus	thymus
9	chr1:170502200-170508400	Weak transcription	Thymus	Thymus
10	chr1:170502200-170521000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:170502400-170512200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:170502400-170514800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:170502600-170507800	Weak transcription	Fetal Lung	lung
14	chr1:170502600-170508400	Weak transcription	Fetal Intestine Small	intestine
15	chr1:170502600-170508600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:170502600-170508600	Weak transcription	Fetal Brain Female	brain
17	chr1:170502600-170509000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:170502600-170509800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:170502600-170510200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:170502600-170510200	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:170502600-170511600	Weak transcription	Brain Substantia Nigra	brain
22	chr1:170502600-170512000	Weak transcription	Aorta	Aorta
23	chr1:170502600-170520800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:170502600-170523400	Weak transcription	Fetal Brain Male	brain
25	chr1:170502800-170507600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr1:170502800-170507800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:170502800-170508200	Weak transcription	Fetal Stomach	stomach
28	chr1:170502800-170508400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:170502800-170508400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:170502800-170508400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr1:170502800-170508400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:170502800-170508400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:170502800-170508400	Weak transcription	Fetal Intestine Large	intestine
34	chr1:170502800-170508800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:170502800-170509600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr1:170502800-170509600	Weak transcription	Brain Germinal Matrix	brain
37	chr1:170502800-170509800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:170502800-170512200	Weak transcription	Brain Anterior Caudate	brain
39	chr1:170502800-170513800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:170503000-170507600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr1:170503000-170507800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:170503000-170507800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr1:170503000-170508000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:170503000-170508000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:170503000-170508200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:170503000-170508200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:170503000-170508200	Weak transcription	Hela-S3	cervix
48	chr1:170503000-170508400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr1:170503000-170508400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:170503000-170508400	Weak transcription	Duodenum Mucosa	Duodenum

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