Variant report

Variant	rs2644889
Chromosome Location	chr19:41320767-41320768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41307688..41310230-chr19:41318329..41321323,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269858	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2545755	0.81[ASN][1000 genomes]
rs2604893	0.81[ASN][1000 genomes]
rs2644898	0.82[ASN][1000 genomes]
rs2644916	0.89[ASN][1000 genomes]
rs4803368	0.81[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	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2758500	chr19:41291627-41546068	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2758762	chr19:41291627-41546068	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1066637	chr19:41309211-41597896	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv521459	chr19:41313202-41333284	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2644889	C19orf54	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41315000-41324400	Weak transcription	HepG2	liver
2	chr19:41315000-41332600	Weak transcription	Aorta	Aorta
3	chr19:41316200-41324400	Weak transcription	Gastric	stomach
4	chr19:41316400-41325400	Weak transcription	Dnd41	blood
5	chr19:41317200-41320800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr19:41317600-41324000	Weak transcription	Hela-S3	cervix
7	chr19:41317600-41324400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:41317800-41324200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr19:41317800-41324400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr19:41317800-41324400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr19:41318000-41324400	Weak transcription	Pancreas	Pancrea
12	chr19:41318000-41324400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr19:41318000-41324400	Weak transcription	Right Atrium	heart
14	chr19:41318200-41323600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:41318200-41323800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:41318200-41324400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:41318400-41321200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:41318400-41322800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr19:41318400-41323200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr19:41318400-41323800	Weak transcription	Primary B cells from cord blood	blood
21	chr19:41318400-41323800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:41318400-41323800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr19:41318600-41323000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr19:41318600-41323800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr19:41318800-41322600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr19:41318800-41323800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:41318800-41324200	Weak transcription	Fetal Intestine Large	intestine
28	chr19:41318800-41324400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:41319000-41323800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr19:41319000-41324400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:41319200-41323800	Weak transcription	Fetal Intestine Small	intestine
32	chr19:41319200-41324000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr19:41319200-41324000	Weak transcription	Lung	lung
34	chr19:41319200-41324200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr19:41319200-41324200	Weak transcription	Adipose Nuclei	Adipose
36	chr19:41319200-41324200	Weak transcription	Brain Anterior Caudate	brain
37	chr19:41319200-41324400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr19:41319200-41324400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr19:41319200-41324400	Weak transcription	NHLF	lung
40	chr19:41319400-41321400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:41319400-41324200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr19:41319400-41324200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr19:41319400-41324200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr19:41319400-41324400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:41319400-41324400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr19:41319400-41324400	Weak transcription	Colonic Mucosa	Colon
47	chr19:41319400-41324400	Weak transcription	Spleen	Spleen
48	chr19:41319800-41323800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr19:41319800-41323800	Weak transcription	Colon Smooth Muscle	Colon
50	chr19:41319800-41324000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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