Variant report

Variant	rs58247981
Chromosome Location	chr19:38870649-38870650
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	POLR2A	chr19:38869050-38873371	K562	blood:	n/a	n/a
2	POLR2A	chr19:38869721-38871433	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr19:38870642-38870689	K562	blood:	n/a	n/a
4	POLR2A	chr19:38869603-38879135	K562	blood:	n/a	n/a
5	POLR2A	chr19:38869822-38870697	GM12892	blood:	n/a	n/a
6	POLR2A	chr19:38869831-38870651	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38824724..38826894-chr19:38868914..38871370,2	MCF-7	breast:
2	chr19:38799413..38800951-chr19:38868296..38871211,2	MCF-7	breast:
3	chr19:38753884..38755807-chr19:38870034..38871603,2	MCF-7	breast:

Variant related genes	Relation type
PSMD8	TF binding region
ENSG00000099338	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000167642	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10153497	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11880285	1.00[AMR][1000 genomes]
rs11881714	1.00[AMR][1000 genomes]
rs2286548	1.00[AMR][1000 genomes]
rs2302185	1.00[AMR][1000 genomes]
rs45589333	1.00[AMR][1000 genomes]
rs57249964	1.00[AMR][1000 genomes]
rs57347571	1.00[AMR][1000 genomes]
rs57361474	1.00[AMR][1000 genomes]
rs58490212	1.00[AMR][1000 genomes]
rs58591078	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59047386	1.00[AMR][1000 genomes]
rs59776537	1.00[AMR][1000 genomes]
rs59845491	1.00[AMR][1000 genomes]
rs60068553	1.00[AMR][1000 genomes]
rs60491875	1.00[AMR][1000 genomes]
rs61648033	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1064275	chr19:38859865-38913251	Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38866400-38876000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:38866800-38871600	Weak transcription	Small Intestine	intestine
3	chr19:38867000-38874600	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr19:38867000-38874800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr19:38867000-38874800	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr19:38867000-38875600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr19:38867000-38877200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:38867000-38878000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr19:38867200-38871600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:38867200-38872000	Weak transcription	Stomach Mucosa	stomach
11	chr19:38867200-38874600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr19:38867200-38874800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:38867200-38874800	Strong transcription	Fetal Intestine Large	intestine
14	chr19:38867200-38875200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr19:38867200-38875400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr19:38867200-38877000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:38867200-38877200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr19:38867200-38877400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:38867400-38871800	Weak transcription	Fetal Brain Male	brain
20	chr19:38867400-38874400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr19:38867400-38875000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr19:38867400-38875800	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr19:38867600-38870800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr19:38867600-38872600	Weak transcription	Fetal Heart	heart
25	chr19:38867600-38872800	Strong transcription	NHEK	skin
26	chr19:38867600-38873000	Strong transcription	Placenta	Placenta
27	chr19:38867600-38873800	Strong transcription	Fetal Stomach	stomach
28	chr19:38867600-38874800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr19:38867600-38874800	Strong transcription	Fetal Muscle Trunk	muscle
30	chr19:38867600-38875200	Strong transcription	Liver	Liver
31	chr19:38867600-38875400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr19:38867600-38875600	Strong transcription	Fetal Intestine Small	intestine
33	chr19:38867600-38875800	Strong transcription	Primary T cells from cord blood	blood
34	chr19:38867600-38876000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr19:38867600-38876200	Strong transcription	Brain Cingulate Gyrus	brain
36	chr19:38867600-38877400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:38867800-38871400	Weak transcription	Hela-S3	cervix
38	chr19:38867800-38871600	Strong transcription	Dnd41	blood
39	chr19:38867800-38871800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr19:38867800-38872200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr19:38867800-38873800	Strong transcription	Fetal Muscle Leg	muscle
42	chr19:38867800-38875000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr19:38867800-38875000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:38867800-38875200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:38867800-38875200	Strong transcription	Thymus	Thymus
46	chr19:38867800-38875400	Strong transcription	Duodenum Mucosa	Duodenum
47	chr19:38867800-38875600	Strong transcription	Colon Smooth Muscle	Colon
48	chr19:38867800-38875800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:38867800-38875800	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr19:38867800-38876200	Strong transcription	Adipose Nuclei	Adipose

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