Variant report

Variant	rs11879838
Chromosome Location	chr19:19742751-19742752
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19702415..19703999-chr19:19742408..19743931,2	MCF-7	breast:
2	chr19:19736608..19739884-chr19:19741504..19746062,6	K562	blood:
3	chr19:19738621..19740217-chr19:19740622..19743235,2	MCF-7	breast:
4	chr19:19742582..19744978-chr19:19752579..19757681,5	MCF-7	breast:
5	chr19:19650041..19652184-chr19:19740271..19743058,2	K562	blood:

Variant related genes	Relation type
ENSG00000089639	Chromatin interaction
ENSG00000160161	Chromatin interaction
ENSG00000064547	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10403759	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11878202	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12976826	0.96[ASN][1000 genomes]
rs16994684	0.95[ASN][1000 genomes]
rs16996174	0.95[ASN][1000 genomes]
rs1968047	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2043293	0.93[ASN][1000 genomes]
rs2304129	0.97[ASN][1000 genomes]
rs34725331	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4808974	0.95[ASN][1000 genomes]
rs7252228	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs739461	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8101679	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8113682	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs880090	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][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	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911309	chr19:19727042-19784891	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19729800-19744400	Weak transcription	HSMMtube	muscle
2	chr19:19735000-19753200	Weak transcription	K562	blood
3	chr19:19738600-19744200	Weak transcription	Liver	Liver
4	chr19:19738600-19753000	Weak transcription	Fetal Brain Male	brain
5	chr19:19738800-19743400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:19738800-19752800	Weak transcription	Stomach Mucosa	stomach
7	chr19:19739000-19743400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr19:19739000-19744000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr19:19739000-19744400	Weak transcription	NHDF-Ad	bronchial
10	chr19:19739000-19745000	Weak transcription	HSMM	muscle
11	chr19:19739600-19744400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr19:19739800-19743200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr19:19739800-19743400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:19739800-19743400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:19739800-19743400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr19:19739800-19743600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr19:19739800-19744000	Weak transcription	Osteobl	bone
18	chr19:19739800-19744200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr19:19739800-19744200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr19:19739800-19744400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr19:19739800-19744600	Weak transcription	Brain Hippocampus Middle	brain
22	chr19:19739800-19744800	Weak transcription	Esophagus	oesophagus
23	chr19:19739800-19744800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr19:19739800-19745000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr19:19739800-19745200	Weak transcription	Right Ventricle	heart
26	chr19:19739800-19745600	Weak transcription	Ovary	ovary
27	chr19:19739800-19752600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr19:19739800-19753200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:19739800-19753400	Weak transcription	Small Intestine	intestine
30	chr19:19739800-19753400	Weak transcription	HMEC	breast
31	chr19:19739800-19753600	Weak transcription	Brain Angular Gyrus	brain
32	chr19:19739800-19753600	Weak transcription	Brain Substantia Nigra	brain
33	chr19:19739800-19753600	Weak transcription	Left Ventricle	heart
34	chr19:19739800-19753600	Weak transcription	Right Atrium	heart
35	chr19:19740000-19743200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr19:19740000-19743400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr19:19740000-19743400	Weak transcription	Adipose Nuclei	Adipose
38	chr19:19740000-19743600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr19:19740000-19743600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr19:19740000-19744000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr19:19740000-19744200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr19:19740000-19744200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr19:19740000-19744200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:19740000-19744200	Weak transcription	Fetal Intestine Large	intestine
45	chr19:19740000-19744400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr19:19740000-19744600	Weak transcription	Gastric	stomach
47	chr19:19740000-19744800	Weak transcription	Colonic Mucosa	Colon
48	chr19:19740000-19744800	Weak transcription	Pancreas	Pancrea
49	chr19:19740000-19745000	Weak transcription	Fetal Lung	lung
50	chr19:19740000-19745000	Weak transcription	Rectal Smooth Muscle	rectum

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