Variant report

Variant	rs3859550
Chromosome Location	chr19:38797946-38797947
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38753031..38764322-chr19:38787496..38798494,54	MCF-7	breast:
2	chr19:38718266..38721870-chr19:38794040..38798765,4	MCF-7	breast:
3	chr19:38779327..38783351-chr19:38794485..38798006,3	K562	blood:
4	chr19:38793982..38798570-chr19:38826004..38829304,4	K562	blood:
5	chr19:38795298..38801659-chr19:38801673..38807893,10	K562	blood:
6	chr19:38744545..38747881-chr19:38796739..38799856,3	K562	blood:
7	chr19:38780526..38782372-chr19:38797679..38799619,2	K562	blood:
8	chr19:38796381..38798650-chr19:38799992..38801610,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000167641	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000167642	Chromatin interaction
ENSG00000267748	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000011332	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11878707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2286550	0.82[CHB][hapmap]
rs34614180	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35077481	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35323359	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35710536	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71354996	1.00[AMR][1000 genomes];0.94[EUR][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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38771400-38805800	Weak transcription	Right Atrium	heart
2	chr19:38781200-38805800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:38782000-38806000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:38782400-38798000	Weak transcription	Fetal Thymus	thymus
5	chr19:38784000-38805800	Weak transcription	Primary B cells from cord blood	blood
6	chr19:38791600-38798000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:38791800-38798000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:38792000-38805400	Weak transcription	NHDF-Ad	bronchial
9	chr19:38792000-38805800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr19:38794400-38800200	Strong transcription	Brain Inferior Temporal Lobe	brain
11	chr19:38794400-38800400	Strong transcription	Aorta	Aorta
12	chr19:38794400-38800400	Strong transcription	Thymus	Thymus
13	chr19:38794400-38800400	Strong transcription	NHLF	lung
14	chr19:38794600-38799400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:38794800-38799600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:38794800-38800400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr19:38795200-38800600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr19:38795200-38805800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr19:38795400-38800000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr19:38795400-38800200	Strong transcription	Brain Germinal Matrix	brain
21	chr19:38795400-38800400	Strong transcription	Dnd41	blood
22	chr19:38795400-38800600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr19:38795400-38800600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr19:38795400-38805800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr19:38795600-38798200	Weak transcription	HSMM	muscle
26	chr19:38795600-38798600	Weak transcription	Fetal Lung	lung
27	chr19:38795600-38798800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr19:38795600-38799000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr19:38795600-38800800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr19:38795600-38805800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr19:38795800-38798000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr19:38795800-38798000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:38795800-38800800	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr19:38795800-38801800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:38796000-38800400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr19:38796000-38800400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:38796000-38800400	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr19:38796000-38803400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:38796200-38798000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:38796200-38798000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr19:38796200-38798000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr19:38796200-38798400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:38796200-38798400	Weak transcription	GM12878-XiMat	blood
44	chr19:38796200-38800000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr19:38796200-38800200	Strong transcription	Liver	Liver
46	chr19:38796200-38804400	Weak transcription	NH-A	brain
47	chr19:38796200-38805400	Weak transcription	HepG2	liver
48	chr19:38796400-38798000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr19:38796400-38798000	Weak transcription	Pancreas	Pancrea
50	chr19:38796400-38798000	Weak transcription	Rectal Mucosa Donor 31	rectum

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