Variant report

Variant	rs34380065
Chromosome Location	chr19:51841417-51841418
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr19:51841384-51841485	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr19:51841320-51841470	GM06990	blood:	n/a	n/a
3	CTCF	chr19:51841280-51841430	GM12871	blood:	n/a	n/a
4	MXI1	chr19:51841395-51844121	SK-N-SH	brain:	n/a	n/a
5	JUN	chr19:51841266-51844229	K562	blood:	n/a	chr19:51842877-51842886 chr19:51842453-51842462 chr19:51842826-51842836 chr19:51843435-51843444

No.	Distal block	Cell Line	Cell type
1	chr19:51841257..51845442-chr19:51896216..51899567,12	K562	blood:
2	chr19:51841314..51846809-chr19:51868154..51872523,19	K562	blood:
3	chr19:51841175..51847735-chr19:51867771..51872496,21	MCF-7	breast:
4	chr19:51841279..51843677-chr19:51919444..51921911,2	K562	blood:
5	chr19:51840838..51845657-chr19:51892354..51900411,18	K562	blood:
6	chr19:51841410..51842759-chr19:51910739..51912174,8	K562	blood:

Variant related genes	Relation type
ENSG00000267905	TF binding region
ENSG00000269403	Chromatin interaction
ENSG00000262874	Chromatin interaction
ENSG00000160318	Chromatin interaction
ENSG00000142512	Chromatin interaction
ENSG00000268889	Chromatin interaction
ENSG00000268520	Chromatin interaction
ENSG00000105379	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1035454	0.89[EUR][1000 genomes]
rs10414211	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10419062	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10424579	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11084068	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878664	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12463376	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011612	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28668475	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6509528	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7259266	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8105710	0.91[EUR][1000 genomes];0.99[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	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1813225	chr19:51821612-51888813	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51831400-51841800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr19:51831600-51841800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr19:51832200-51841600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr19:51832400-51841800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:51833000-51842000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr19:51833600-51842000	Weak transcription	Brain Substantia Nigra	brain
7	chr19:51834200-51842200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:51834400-51841800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr19:51834600-51841800	Weak transcription	Fetal Intestine Large	intestine
10	chr19:51834800-51841800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr19:51834800-51842000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr19:51834800-51842200	Weak transcription	Gastric	stomach
13	chr19:51834800-51842200	Weak transcription	Pancreas	Pancrea
14	chr19:51835000-51841800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:51835000-51841800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:51835000-51841800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr19:51835000-51842200	Weak transcription	Left Ventricle	heart
18	chr19:51835600-51841800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr19:51835600-51841800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr19:51835600-51841800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr19:51835800-51841800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr19:51835800-51841800	Weak transcription	Liver	Liver
23	chr19:51835800-51841800	Weak transcription	Fetal Intestine Small	intestine
24	chr19:51835800-51842200	Weak transcription	Aorta	Aorta
25	chr19:51836000-51841800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr19:51836000-51842000	Weak transcription	Brain Hippocampus Middle	brain
27	chr19:51836000-51842000	Weak transcription	Ovary	ovary
28	chr19:51836200-51842000	Weak transcription	HepG2	liver
29	chr19:51836600-51841600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:51837600-51841800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr19:51837600-51841800	Weak transcription	A549	lung
32	chr19:51837600-51842200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:51838800-51841800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:51838800-51841800	Weak transcription	Brain Germinal Matrix	brain
35	chr19:51839200-51841800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr19:51839400-51841800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:51840800-51842000	Weak transcription	Esophagus	oesophagus
38	chr19:51841000-51841600	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr19:51841200-51841600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr19:51841200-51841600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:51841200-51841800	Enhancers	H1 Cell Line	embryonic stem cell
42	chr19:51841200-51841800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr19:51841200-51842000	Enhancers	Primary hematopoietic stem cells	blood
44	chr19:51841200-51842200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr19:51841200-51842200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:51841400-51841800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:51841400-51841800	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr19:51841400-51841800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr19:51841400-51841800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:51841400-51841800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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