Variant report

Variant	rs28625452
Chromosome Location	chr19:42956028-42956029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42954091..42956450-chr19:43031167..43032673,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079385	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10401428	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs10402853	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10403065	0.93[AMR][1000 genomes]
rs10405152	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10405179	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10405410	0.93[AMR][1000 genomes]
rs10405891	0.81[AMR][1000 genomes]
rs10405942	0.93[AMR][1000 genomes]
rs10406227	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10408822	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10414396	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10414969	0.81[AMR][1000 genomes]
rs10416108	0.93[AMR][1000 genomes]
rs10416915	0.81[AMR][1000 genomes]
rs10417560	0.81[AMR][1000 genomes]
rs10418090	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10418997	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10419561	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs10422191	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423227	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10424206	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11879033	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11881583	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11882225	0.93[AMR][1000 genomes]
rs11882291	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11882701	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13343840	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13345272	0.93[AMR][1000 genomes]
rs13345659	0.81[AMR][1000 genomes]
rs16975743	0.81[AMR][1000 genomes]
rs16975750	0.81[AMR][1000 genomes]
rs16975787	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16975799	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975815	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16975862	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2051832	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2051833	0.93[AMR][1000 genomes]
rs28403155	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28425201	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs28448880	0.81[AMR][1000 genomes]
rs28473486	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs28588100	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs35623577	0.81[AMR][1000 genomes]
rs57018456	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58050143	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58162305	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58702905	1.00[EUR][1000 genomes]
rs61388144	0.81[AFR][1000 genomes]
rs6509019	0.93[AMR][1000 genomes]
rs7248439	0.81[AMR][1000 genomes]
rs7248907	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7249304	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7252874	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7255271	0.93[AMR][1000 genomes]
rs7256226	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs73560408	0.81[AFR][1000 genomes]
rs8101378	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8104731	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8107720	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8110922	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9916999	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9917002	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42948200-42956800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr19:42952000-42957600	Enhancers	HepG2	liver
3	chr19:42952400-42964400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr19:42953400-42956600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr19:42953400-42957200	Enhancers	Duodenum Mucosa	Duodenum
6	chr19:42953600-42957800	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr19:42954000-42957200	Weak transcription	Lung	lung
8	chr19:42954200-42956400	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr19:42954200-42957800	Enhancers	Primary hematopoietic stem cells	blood
10	chr19:42954200-42959000	Weak transcription	Small Intestine	intestine
11	chr19:42954400-42957600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:42954400-42957800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:42954400-42961000	Enhancers	Primary B cells from cord blood	blood
14	chr19:42954600-42956200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:42954600-42960000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:42954600-42961600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr19:42954800-42956200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr19:42954800-42956200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr19:42954800-42956600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr19:42954800-42956600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr19:42954800-42956600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr19:42954800-42959200	Weak transcription	HMEC	breast
23	chr19:42955000-42956800	Enhancers	Colonic Mucosa	Colon
24	chr19:42955200-42956600	Weak transcription	Left Ventricle	heart
25	chr19:42955200-42959200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr19:42955200-42959800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:42955400-42956600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr19:42955400-42956800	Weak transcription	Adipose Nuclei	Adipose
29	chr19:42955400-42957000	Weak transcription	Fetal Intestine Small	intestine
30	chr19:42955400-42964000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr19:42955400-42964600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr19:42955600-42956600	Weak transcription	Fetal Intestine Large	intestine
33	chr19:42955600-42959000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr19:42955600-42959400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr19:42955800-42956200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:42955800-42957000	Enhancers	Primary B cells from peripheral blood	blood
37	chr19:42955800-42959200	Weak transcription	Stomach Mucosa	stomach
38	chr19:42955800-42966400	Weak transcription	GM12878-XiMat	blood
39	chr19:42956000-42957400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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