Variant report

Variant	rs485980
Chromosome Location	chr19:37414589-37414590
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37405380..37408333-chr19:37412047..37415045,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198453	Chromatin interaction
ENSG00000185869	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1069756	0.82[AFR][1000 genomes]
rs1069757	0.82[AFR][1000 genomes]
rs1148397	0.81[AFR][1000 genomes]
rs1644644	0.91[AFR][1000 genomes]
rs1644646	0.91[AFR][1000 genomes]
rs1644653	0.85[AFR][1000 genomes]
rs1644655	0.85[AFR][1000 genomes]
rs1644680	0.85[AFR][1000 genomes]
rs1644694	0.85[AFR][1000 genomes]
rs1644703	0.82[AFR][1000 genomes]
rs1644709	0.97[AFR][1000 genomes]
rs1667332	0.91[AFR][1000 genomes]
rs1667334	0.91[AFR][1000 genomes]
rs1667361	0.85[AFR][1000 genomes]
rs1667362	0.85[AFR][1000 genomes]
rs2435066	0.82[AFR][1000 genomes]
rs2562584	0.82[AFR][1000 genomes]
rs2562586	0.82[AFR][1000 genomes]
rs2562588	0.82[AFR][1000 genomes]
rs35624635	0.85[AFR][1000 genomes]
rs477893	0.91[AFR][1000 genomes]
rs486891	0.97[AFR][1000 genomes]
rs549031	0.91[AFR][1000 genomes]
rs555433	0.81[AFR][1000 genomes]
rs565030	0.81[AFR][1000 genomes]
rs569068	0.97[AFR][1000 genomes]
rs573596	0.97[AFR][1000 genomes]
rs577844	0.97[AFR][1000 genomes]
rs703528	0.82[AFR][1000 genomes]
rs703529	0.82[AFR][1000 genomes]
rs703532	0.82[AFR][1000 genomes]
rs703533	0.82[AFR][1000 genomes]
rs703534	0.82[AFR][1000 genomes]
rs703536	0.82[AFR][1000 genomes]
rs7255728	0.85[AFR][1000 genomes]
rs8102364	0.82[AFR][1000 genomes]
rs826286	0.97[AFR][1000 genomes]
rs826287	0.97[AFR][1000 genomes]
rs862248	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv521605	chr19:37261810-37483444	ZNF genes & repeats Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv1060155	chr19:37274915-37458788	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv544000	chr19:37274915-37458788	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
13	nsv911651	chr19:37300554-37428465	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
15	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
16	nsv523848	chr19:37357289-37487632	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37408200-37436400	Weak transcription	Fetal Thymus	thymus
2	chr19:37408200-37440600	Weak transcription	Stomach Mucosa	stomach
3	chr19:37408400-37417000	Weak transcription	Fetal Kidney	kidney
4	chr19:37408400-37440600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:37408600-37439600	Weak transcription	Fetal Heart	heart
6	chr19:37408800-37414800	Strong transcription	Fetal Muscle Trunk	muscle
7	chr19:37408800-37415200	Strong transcription	Left Ventricle	heart
8	chr19:37409000-37414800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr19:37409000-37415000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:37409000-37444800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:37409000-37447400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:37409200-37414600	Strong transcription	Fetal Lung	lung
13	chr19:37409200-37415000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:37409400-37414800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
15	chr19:37409400-37415000	Strong transcription	Stomach Smooth Muscle	stomach
16	chr19:37409600-37423600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr19:37409800-37416000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr19:37409800-37421400	Weak transcription	Fetal Brain Male	brain
19	chr19:37410000-37415400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr19:37410200-37415000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr19:37410600-37416800	Weak transcription	Psoas Muscle	Psoas
22	chr19:37410600-37417200	Weak transcription	NHLF	lung
23	chr19:37410600-37427600	Weak transcription	NH-A	brain
24	chr19:37411600-37414800	ZNF genes & repeats	Liver	Liver
25	chr19:37411600-37414800	Strong transcription	Brain Germinal Matrix	brain
26	chr19:37411600-37418000	Strong transcription	NHDF-Ad	bronchial
27	chr19:37411800-37414600	Strong transcription	Placenta	Placenta
28	chr19:37411800-37414800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:37411800-37414800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
30	chr19:37411800-37415000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
31	chr19:37411800-37418600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
32	chr19:37412600-37414800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:37412600-37414800	ZNF genes & repeats	Primary B cells from cord blood	blood
34	chr19:37412600-37414800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
35	chr19:37412600-37418600	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr19:37412600-37419600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
37	chr19:37412800-37414600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
38	chr19:37412800-37414800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
39	chr19:37412800-37415000	ZNF genes & repeats	Adipose Nuclei	Adipose
40	chr19:37412800-37417400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:37413000-37414800	Strong transcription	Primary B cells from peripheral blood	blood
42	chr19:37413000-37415000	Strong transcription	Brain Cingulate Gyrus	brain
43	chr19:37413000-37415000	ZNF genes & repeats	Colon Smooth Muscle	Colon
44	chr19:37413000-37416600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr19:37413400-37414800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
46	chr19:37413400-37414800	Strong transcription	HSMM	muscle
47	chr19:37413600-37415000	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
48	chr19:37413600-37421400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr19:37413600-37427600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr19:37413800-37414800	Strong transcription	Rectal Mucosa Donor 29	rectum

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