Variant report

Variant	rs28534944
Chromosome Location	chr19:45301088-45301089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:45256739..45258538-chr19:45300168..45301873,2	MCF-7	breast:
2	chr19:45297988..45303860-chr19:45347133..45351877,8	MCF-7	breast:
3	chr19:45298818..45303552-chr19:45309335..45312129,4	MCF-7	breast:
4	chr19:45299139..45302244-chr19:45346521..45349323,3	MCF-7	breast:
5	chr19:45251065..45253073-chr19:45300378..45301939,2	MCF-7	breast:
6	chr19:45297303..45299593-chr19:45300939..45303324,2	K562	blood:
7	chr19:45300140..45302354-chr19:45327426..45329957,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130202	Chromatin interaction
ENSG00000069399	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10408993	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1075643	0.85[EUR][1000 genomes]
rs2927478	0.87[EUR][1000 genomes]
rs2927479	0.87[EUR][1000 genomes]
rs2965161	0.87[EUR][1000 genomes]
rs2967671	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3810140	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3810141	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7249750	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73572003	0.84[ASN][1000 genomes]
rs73572006	0.91[EUR][1000 genomes]
rs8113171	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833841	chr19:45208486-45308043	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	nsv912117	chr19:45298069-45322744	Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv912118	chr19:45300056-45326664	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45281400-45311400	Weak transcription	Right Atrium	heart
2	chr19:45284600-45309800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:45284800-45303400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr19:45284800-45311400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr19:45285200-45304000	Strong transcription	NHEK	skin
6	chr19:45288000-45303200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr19:45288000-45303200	Weak transcription	Spleen	Spleen
8	chr19:45290600-45303400	Strong transcription	Fetal Intestine Large	intestine
9	chr19:45292000-45302400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:45292000-45302800	Strong transcription	HMEC	breast
11	chr19:45294200-45311600	Weak transcription	Small Intestine	intestine
12	chr19:45295400-45302600	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr19:45296200-45310600	Weak transcription	Colonic Mucosa	Colon
14	chr19:45296400-45303200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr19:45296800-45311000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:45297000-45303200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr19:45297000-45307200	Weak transcription	Lung	lung
18	chr19:45297000-45311800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr19:45297400-45301200	Weak transcription	Esophagus	oesophagus
20	chr19:45297600-45303600	Weak transcription	Fetal Stomach	stomach
21	chr19:45298200-45310200	Weak transcription	Gastric	stomach
22	chr19:45299000-45301400	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr19:45299000-45303200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr19:45299200-45301200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr19:45299200-45301400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr19:45299200-45303400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:45299200-45303400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr19:45299200-45307200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr19:45299200-45310200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr19:45299400-45301800	Enhancers	HUVEC	blood vessel
31	chr19:45299600-45301400	Enhancers	Pancreas	Pancrea
32	chr19:45299800-45301600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:45300200-45302800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr19:45300400-45301400	Weak transcription	NH-A	brain
35	chr19:45300400-45302000	Weak transcription	Placenta	Placenta
36	chr19:45300400-45303400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:45300400-45303600	Weak transcription	Left Ventricle	heart
38	chr19:45300400-45304000	Enhancers	A549	lung
39	chr19:45300600-45301200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr19:45300600-45301200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr19:45300600-45301800	Weak transcription	GM12878-XiMat	blood
42	chr19:45300600-45303000	Enhancers	HepG2	liver
43	chr19:45300600-45303200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr19:45300600-45303200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:45300600-45303200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr19:45300600-45303200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:45300600-45303200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr19:45300600-45303200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:45300600-45303200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:45300600-45303200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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