Variant report

Variant	rs7249939
Chromosome Location	chr19:38792143-38792144
allele	C/G
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	chr19:38790918-38797378	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:38790968-38797461	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38753031..38764322-chr19:38787496..38798494,54	MCF-7	breast:
2	chr12:46762605..46765177-chr19:38791168..38793279,2	MCF-7	breast:
3	chr19:38791989..38796796-chr19:38825093..38829391,7	MCF-7	breast:
4	chr19:38786777..38792864-chr19:38793393..38797878,11	K562	blood:

Variant related genes	Relation type
C19orf33	TF binding region
ENSG00000167644	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000167642	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs3786881	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7246583	1.00[AMR][1000 genomes]
rs7247591	1.00[AMR][1000 genomes]
rs8104432	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv960928	chr19:38790012-38822380	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38765800-38794800	Weak transcription	Small Intestine	intestine
2	chr19:38769400-38795200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr19:38771400-38805800	Weak transcription	Right Atrium	heart
4	chr19:38781000-38794400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr19:38781200-38795800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr19:38781200-38805800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr19:38781400-38795400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr19:38781400-38797800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr19:38781600-38795600	Weak transcription	Right Ventricle	heart
10	chr19:38782000-38806000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr19:38782400-38798000	Weak transcription	Fetal Thymus	thymus
12	chr19:38782600-38796400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr19:38783000-38794200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr19:38783000-38795600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr19:38783200-38794200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr19:38783400-38797000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr19:38783600-38795200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr19:38784000-38794600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr19:38784000-38797200	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr19:38784000-38805800	Weak transcription	Primary B cells from cord blood	blood
21	chr19:38784200-38793400	Weak transcription	Lung	lung
22	chr19:38784200-38794200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr19:38784200-38794400	Weak transcription	Thymus	Thymus
24	chr19:38784400-38794400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr19:38785200-38795200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:38785200-38795400	Weak transcription	Primary T cells from cord blood	blood
27	chr19:38785200-38795400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr19:38785400-38794200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr19:38785400-38794400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr19:38785400-38794600	Weak transcription	Brain Substantia Nigra	brain
31	chr19:38785400-38794800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr19:38785400-38795400	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr19:38785400-38797000	Weak transcription	Brain Anterior Caudate	brain
34	chr19:38785600-38794400	Weak transcription	Brain Angular Gyrus	brain
35	chr19:38785600-38794800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr19:38785800-38794000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr19:38785800-38794200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr19:38785800-38794200	Weak transcription	Brain Hippocampus Middle	brain
39	chr19:38788000-38793400	Enhancers	NHEK	skin
40	chr19:38789600-38794400	Weak transcription	Aorta	Aorta
41	chr19:38790000-38797800	Weak transcription	Ovary	ovary
42	chr19:38790200-38793000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr19:38790200-38793200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr19:38790200-38794600	Weak transcription	Adipose Nuclei	Adipose
45	chr19:38790400-38793000	Enhancers	Fetal Intestine Small	intestine
46	chr19:38790400-38794000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr19:38790400-38794200	Enhancers	Fetal Intestine Large	intestine
48	chr19:38791200-38792600	Enhancers	Muscle Satellite Cultured Cells	--
49	chr19:38791200-38792600	Enhancers	HSMM	muscle
50	chr19:38791200-38792600	Enhancers	NHLF	lung

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