Variant report

Variant	rs28427504
Chromosome Location	chr19:40959852-40959853
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	chr19:40949023..40953581-chr19:40954175..40961322,7	MCF-7	breast:
2	chr19:40958062..40959983-chr19:41114134..41116969,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268366	Chromatin interaction
ENSG00000090006	Chromatin interaction
ENSG00000167565	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11878466	0.83[AMR][1000 genomes]
rs7256097	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv911708	chr19:40855255-40982375	Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
5	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
6	nsv911709	chr19:40928944-41060616	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv911710	chr19:40954062-40978869	Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv911711	chr19:40954062-40985003	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv911712	chr19:40957734-40978869	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv911713	chr19:40957734-40981198	Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40951000-40970200	Weak transcription	Small Intestine	intestine
2	chr19:40951000-40970400	Weak transcription	Fetal Heart	heart
3	chr19:40951000-40970600	Weak transcription	Psoas Muscle	Psoas
4	chr19:40951000-40971200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:40951200-40961200	Weak transcription	Thymus	Thymus
6	chr19:40951200-40967000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr19:40951200-40969000	Weak transcription	NHDF-Ad	bronchial
8	chr19:40951200-40969800	Weak transcription	Right Atrium	heart
9	chr19:40951200-40970400	Weak transcription	Brain Angular Gyrus	brain
10	chr19:40951200-40970400	Weak transcription	Brain Substantia Nigra	brain
11	chr19:40951200-40970400	Weak transcription	HSMMtube	muscle
12	chr19:40951200-40970400	Weak transcription	NH-A	brain
13	chr19:40951200-40970600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:40951200-40970600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr19:40951600-40967000	Strong transcription	Fetal Intestine Small	intestine
16	chr19:40952000-40965000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr19:40952000-40969000	Weak transcription	Osteobl	bone
18	chr19:40952000-40970000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr19:40952000-40970400	Weak transcription	NHLF	lung
20	chr19:40952200-40965000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr19:40952200-40970800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr19:40952400-40963600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr19:40952400-40963800	Weak transcription	Colonic Mucosa	Colon
24	chr19:40952400-40970600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr19:40952400-40970600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr19:40952600-40965400	Strong transcription	Liver	Liver
27	chr19:40952600-40967000	Weak transcription	Stomach Mucosa	stomach
28	chr19:40952600-40970600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr19:40953600-40961600	Strong transcription	Fetal Muscle Leg	muscle
30	chr19:40954200-40963200	Weak transcription	Pancreas	Pancrea
31	chr19:40954200-40963600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr19:40954200-40969000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:40954200-40970400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr19:40954400-40961200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr19:40954400-40963200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:40954400-40963600	Weak transcription	Left Ventricle	heart
37	chr19:40954400-40967800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr19:40954400-40969800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr19:40954400-40970400	Weak transcription	Brain Hippocampus Middle	brain
40	chr19:40954400-40970400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr19:40954600-40963000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr19:40954800-40962000	Weak transcription	Right Ventricle	heart
43	chr19:40954800-40963200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr19:40954800-40963600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr19:40954800-40970200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr19:40954800-40970400	Weak transcription	Aorta	Aorta
47	chr19:40954800-40970400	Weak transcription	Brain Anterior Caudate	brain
48	chr19:40955000-40963200	Weak transcription	Gastric	stomach
49	chr19:40955000-40963200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr19:40955000-40963600	Weak transcription	Esophagus	oesophagus

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