Variant report

Variant	rs11879872
Chromosome Location	chr19:39395331-39395332
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr19:39395211-39395534	A549	lung:	n/a	n/a
2	CEBPB	chr19:39395220-39395519	HepG2	liver:	n/a	n/a
3	NR2F2	chr19:39395245-39395984	MCF-7	breast:	n/a	n/a
4	FOXA2	chr19:39395194-39395795	A549	lung:	n/a	n/a
5	FOXA2	chr19:39395276-39395853	A549	lung:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39388731..39393423-chr19:39394024..39400037,10	K562	blood:
2	chr19:39337724..39340689-chr19:39393839..39396661,3	K562	blood:
3	chr19:39390244..39393015-chr19:39395233..39398542,3	MCF-7	breast:
4	chr19:39394310..39397205-chr19:39405071..39408067,2	K562	blood:
5	chr19:39394709..39398675-chr19:39410709..39413256,3	K562	blood:
6	chr19:39394465..39398073-chr19:39398218..39402853,5	MCF-7	breast:
7	chr19:39217426..39220275-chr19:39394811..39396577,2	K562	blood:

No data

Variant related genes	Relation type
SIRT2	TF binding region
ENSG00000130402	Chromatin interaction
ENSG00000104825	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000262484	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000068903	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11083484	0.86[ASN][1000 genomes]
rs12979755	0.86[YRI][hapmap]
rs2053071	0.82[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2241705	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3136641	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803006	0.86[YRI][hapmap]
rs8108039	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv1798153	chr19:39338663-39399277	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv911674	chr19:39391547-39398631	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv911675	chr19:39394271-39398631	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11879872	CD177	cis	cerebellum	SCAN
rs11879872	ZNF780B	cis	cerebellum	SCAN
rs11879872	IGFL2	cis	parietal	SCAN
rs11879872	SARS2	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39391000-39395800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr19:39391200-39395400	Weak transcription	Aorta	Aorta
3	chr19:39391200-39395400	Weak transcription	Esophagus	oesophagus
4	chr19:39391200-39395600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr19:39391200-39420800	Weak transcription	Small Intestine	intestine
6	chr19:39391400-39395600	Weak transcription	Brain Germinal Matrix	brain
7	chr19:39391400-39397400	Weak transcription	Fetal Brain Female	brain
8	chr19:39391400-39397600	Weak transcription	Psoas Muscle	Psoas
9	chr19:39391400-39402200	Weak transcription	Fetal Brain Male	brain
10	chr19:39391600-39397800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:39391600-39414800	Weak transcription	HMEC	breast
12	chr19:39391600-39420600	Weak transcription	Right Atrium	heart
13	chr19:39391800-39395400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr19:39391800-39395400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:39391800-39395400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr19:39391800-39395600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:39391800-39395600	Weak transcription	NHLF	lung
18	chr19:39391800-39395800	Weak transcription	Brain Angular Gyrus	brain
19	chr19:39391800-39395800	Weak transcription	HSMMtube	muscle
20	chr19:39391800-39396000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr19:39391800-39396200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr19:39391800-39397400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr19:39391800-39397400	Weak transcription	Fetal Kidney	kidney
24	chr19:39391800-39397600	Weak transcription	HSMM	muscle
25	chr19:39391800-39397800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:39391800-39399000	Weak transcription	NH-A	brain
27	chr19:39391800-39399600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr19:39391800-39400400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr19:39391800-39401800	Weak transcription	Fetal Lung	lung
30	chr19:39391800-39412200	Weak transcription	Osteobl	bone
31	chr19:39392000-39395600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:39392000-39399600	Weak transcription	K562	blood
33	chr19:39392200-39398400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr19:39392400-39395400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr19:39392400-39395600	Weak transcription	Fetal Intestine Large	intestine
36	chr19:39392400-39395800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr19:39392400-39397200	Weak transcription	HUVEC	blood vessel
38	chr19:39392400-39399400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr19:39392400-39414800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:39392600-39395400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr19:39392600-39395400	Weak transcription	Hela-S3	cervix
42	chr19:39392600-39396000	Weak transcription	Stomach Mucosa	stomach
43	chr19:39392600-39396400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr19:39392600-39397400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr19:39392600-39406000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr19:39392600-39414600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr19:39392600-39418800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr19:39392800-39395800	Weak transcription	Fetal Thymus	thymus
49	chr19:39393600-39400200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:39393800-39400200	Strong transcription	Primary B cells from cord blood	blood

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