Variant report

Variant	rs12978311
Chromosome Location	chr19:40025826-40025827
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39934791..39938517-chr19:40022234..40026334,4	K562	blood:
2	chr19:40009271..40012163-chr19:40025249..40026752,2	K562	blood:
3	chr19:40023614..40026391-chr19:40028689..40031990,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176396	Chromatin interaction
ENSG00000196235	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12608773	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12610740	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12610751	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12610833	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12972285	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12972675	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12973775	0.81[AMR][1000 genomes]
rs12980249	0.86[AMR][1000 genomes]
rs1368469	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17795475	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs34271968	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34856311	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs34885802	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs35038530	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3746086	0.85[AMR][1000 genomes]
rs4803258	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4803259	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55994613	0.81[AMR][1000 genomes]
rs59485553	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60587381	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7247184	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7247218	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7257553	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7257904	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7258348	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv911691	chr19:39979966-40029386	Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv911692	chr19:39979966-40046863	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1060251	chr19:39982988-40099773	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv911693	chr19:39986241-40033574	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv579509	chr19:40004640-40133438	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv911694	chr19:40015907-40031369	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv137930	chr19:40019489-40027856	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv961216	chr19:40025191-40026552	Weak transcription Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40023600-40027000	Weak transcription	Fetal Lung	lung
2	chr19:40023600-40028800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr19:40023600-40028800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr19:40023600-40029000	Weak transcription	NHDF-Ad	bronchial
5	chr19:40023600-40029200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:40023600-40029200	Weak transcription	HSMM	muscle
7	chr19:40023600-40029800	Weak transcription	Aorta	Aorta
8	chr19:40023600-40029800	Weak transcription	Left Ventricle	heart
9	chr19:40023800-40028400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr19:40023800-40028400	Weak transcription	GM12878-XiMat	blood
11	chr19:40023800-40028600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr19:40023800-40028800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:40023800-40028800	Weak transcription	Brain Substantia Nigra	brain
14	chr19:40023800-40028800	Weak transcription	Fetal Brain Male	brain
15	chr19:40023800-40029000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:40023800-40029000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr19:40023800-40029000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr19:40023800-40029000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr19:40023800-40029000	Weak transcription	HMEC	breast
20	chr19:40023800-40029000	Weak transcription	Osteobl	bone
21	chr19:40023800-40029200	Weak transcription	Primary B cells from cord blood	blood
22	chr19:40023800-40029200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr19:40023800-40029200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:40023800-40029200	Weak transcription	Adipose Nuclei	Adipose
25	chr19:40023800-40029200	Weak transcription	Fetal Brain Female	brain
26	chr19:40023800-40029200	Weak transcription	Fetal Heart	heart
27	chr19:40023800-40029200	Weak transcription	Fetal Kidney	kidney
28	chr19:40024000-40027400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr19:40024000-40028200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr19:40024000-40028400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:40024000-40028400	Weak transcription	Brain Anterior Caudate	brain
32	chr19:40024000-40028400	Weak transcription	Brain Germinal Matrix	brain
33	chr19:40024000-40028400	Weak transcription	Dnd41	blood
34	chr19:40024000-40028600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr19:40024000-40028800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr19:40024000-40028800	Weak transcription	Liver	Liver
37	chr19:40024000-40028800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr19:40024000-40028800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:40024000-40029000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr19:40024000-40029000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr19:40024000-40029000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:40024000-40029000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr19:40024000-40029000	Weak transcription	Colon Smooth Muscle	Colon
44	chr19:40024000-40029000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr19:40024000-40029000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr19:40024000-40029200	Weak transcription	Primary B cells from peripheral blood	blood
47	chr19:40024000-40029200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr19:40024000-40029600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr19:40024000-40029600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr19:40024000-40029600	Weak transcription	Fetal Stomach	stomach

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