Variant report

Variant	rs2561553
Chromosome Location	chr19:41169518-41169519
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:41167967..41170914-chr19:41255476..41260607,5	K562	blood:
2	chr19:41168873..41171001-chr19:41337568..41339858,2	MCF-7	breast:
3	chr19:41167992..41170856-chr19:41220892..41222830,4	MCF-7	breast:
4	chr19:41167496..41181822-chr19:41192475..41200102,20	MCF-7	breast:
5	chr19:41167287..41169951-chr19:41180209..41183939,4	K562	blood:
6	chr19:41167372..41175149-chr19:41187518..41198541,22	K562	blood:
7	chr19:41167522..41169643-chr19:41327340..41330313,2	K562	blood:
8	chr19:41166318..41173902-chr19:41219711..41223853,11	K562	blood:
9	chr19:41167412..41170593-chr19:41311083..41314714,4	K562	blood:
10	chr19:41168336..41169802-chr19:41208137..41209143,10	K562	blood:
11	chr19:41167276..41170716-chr19:41255553..41260607,5	K562	blood:
12	chr19:41169432..41172402-chr19:41316394..41319342,2	K562	blood:
13	chr19:41167397..41170684-chr19:41303413..41305834,3	K562	blood:
14	chr19:41168190..41170957-chr19:41311771..41313927,2	MCF-7	breast:
15	chr19:41168219..41171584-chr19:41206436..41210632,6	K562	blood:
16	chr19:41167978..41171618-chr19:41220706..41223395,4	K562	blood:
17	chr19:41169093..41170833-chr19:41311173..41313608,2	K562	blood:
18	chr19:41168092..41172340-chr19:41281558..41285076,7	K562	blood:
19	chr19:41168026..41170815-chr19:41206453..41210632,5	K562	blood:
20	chr19:41167265..41169750-chr19:41244881..41246475,2	K562	blood:
21	chr19:41169408..41172450-chr19:41308239..41311343,3	MCF-7	breast:
22	chr19:41075641..41077169-chr19:41168899..41171390,2	K562	blood:
23	chr19:41167833..41170600-chr19:41173317..41176394,3	MCF-7	breast:
24	chr19:41168010..41170261-chr19:41227028..41229783,2	MCF-7	breast:
25	chr19:41169091..41170622-chr19:41170887..41173199,2	MCF-7	breast:
26	chr19:41166820..41170120-chr19:41221252..41223641,4	MCF-7	breast:
27	chr19:41168879..41172340-chr19:41281648..41285076,4	K562	blood:
28	chr19:41165880..41175149-chr19:41192911..41198858,17	K562	blood:
29	chr19:41167628..41170437-chr19:41315910..41318446,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000171570	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000233622	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000160460	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000188493	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2561554	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2561556	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2604878	0.89[CEU][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes]
rs73546860	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1064699	chr19:41086506-41174259	Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv870022	chr19:41113071-41178982	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	diseases
9	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv2489	chr19:41145034-41182170	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv1058707	chr19:41146147-41200820	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41168400-41169600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
2	chr19:41168400-41170000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
3	chr19:41168400-41170000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:41168600-41169600	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr19:41168600-41169600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr19:41168600-41169600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:41168600-41169600	Active TSS	HSMM	muscle
8	chr19:41168600-41169600	Active TSS	NHLF	lung
9	chr19:41168600-41169800	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr19:41168600-41170000	Active TSS	H9 Cell Line	embryonic stem cell
11	chr19:41168600-41170200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr19:41168800-41169600	Active TSS	H1 Cell Line	embryonic stem cell
13	chr19:41168800-41169600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:41168800-41169600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:41168800-41169600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:41168800-41169600	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr19:41168800-41169600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:41168800-41169600	Active TSS	Primary T cells from cord blood	blood
19	chr19:41168800-41169600	Active TSS	Aorta	Aorta
20	chr19:41168800-41169600	Active TSS	Colon Smooth Muscle	Colon
21	chr19:41168800-41169600	Active TSS	Fetal Brain Female	brain
22	chr19:41168800-41169600	Active TSS	Fetal Kidney	kidney
23	chr19:41168800-41169600	Active TSS	Fetal Lung	lung
24	chr19:41168800-41169600	Flanking Active TSS	Fetal Thymus	thymus
25	chr19:41168800-41169600	Active TSS	Left Ventricle	heart
26	chr19:41168800-41169600	Active TSS	Ovary	ovary
27	chr19:41168800-41169600	Active TSS	Placenta Amnion	Placenta Amnion
28	chr19:41168800-41169600	Active TSS	Rectal Smooth Muscle	rectum
29	chr19:41168800-41169600	Active TSS	Right Atrium	heart
30	chr19:41168800-41169600	Active TSS	Right Ventricle	heart
31	chr19:41168800-41169600	Active TSS	Sigmoid Colon	Sigmoid Colon
32	chr19:41168800-41169600	Active TSS	Small Intestine	intestine
33	chr19:41168800-41169600	Active TSS	Spleen	Spleen
34	chr19:41168800-41169800	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr19:41168800-41169800	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr19:41168800-41169800	Active TSS	Brain Substantia Nigra	brain
37	chr19:41168800-41169800	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr19:41168800-41169800	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr19:41168800-41169800	Active TSS	Psoas Muscle	Psoas
40	chr19:41168800-41169800	Flanking Active TSS	Dnd41	blood
41	chr19:41168800-41170000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr19:41168800-41170000	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr19:41168800-41170000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr19:41168800-41170000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:41169000-41169600	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr19:41169000-41169600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr19:41169000-41169600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:41169000-41169800	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr19:41169000-41169800	Flanking Active TSS	Placenta	Placenta
50	chr19:41169000-41170000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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