Variant report

Variant	rs3780439
Chromosome Location	chr9:101078220-101078221
allele	A/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:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:101078185..101080834-chr9:101469551..101472431,2	K562	blood:
2	chr9:101077531..101078224-chr9:101537912..101538518,3	MCF-7	breast:
3	chr9:101070579..101073591-chr9:101076842..101079263,3	MCF-7	breast:
4	chr9:101076029..101078815-chr9:101516431..101518577,2	MCF-7	breast:
5	chr9:101077545..101078479-chr9:101537869..101538795,4	K562	blood:
6	chr9:101077361..101079468-chr9:101293328..101295468,2	K562	blood:
7	chr9:101076714..101079334-chr9:101138741..101140975,3	K562	blood:
8	chr9:101077814..101081761-chr9:101084202..101087593,3	K562	blood:
9	chr9:101077608..101078459-chr9:101336024..101336612,2	MCF-7	breast:
10	chr9:101078079..101080070-chr9:101458096..101460351,2	K562	blood:
11	chr9:101077537..101078267-chr9:101507908..101508672,2	MCF-7	breast:
12	chr9:101077698..101078261-chr9:101181216..101181803,2	MCF-7	breast:
13	chr9:101077617..101078489-chr9:101558428..101559307,2	MCF-7	breast:
14	chr9:101077916..101078459-chr9:101507514..101508218,2	MCF-7	breast:
15	chr9:101077395..101078268-chr9:101530249..101530829,3	MCF-7	breast:
16	chr9:101076038..101079314-chr9:101086093..101088880,3	K562	blood:
17	chr9:101077513..101078805-chr9:101536863..101538719,11	MCF-7	breast:
18	chr9:101077202..101078311-chr9:101536603..101537623,3	MCF-7	breast:
19	chr9:101077809..101079524-chr9:101207949..101210400,2	MCF-7	breast:
20	chr9:101077617..101078376-chr9:101246635..101247206,2	MCF-7	breast:
21	chr9:101077561..101078510-chr9:101535798..101536902,3	K562	blood:
22	chr9:101077527..101078492-chr9:101298829..101299830,3	K562	blood:
23	chr9:101077049..101078493-chr9:101285520..101286892,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000136928	Chromatin interaction
ENSG00000165138	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10760263	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10818756	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs10985815	0.83[EUR][1000 genomes]
rs10985816	0.83[EUR][1000 genomes]
rs3780441	0.81[GIH][hapmap]
rs3780446	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7848116	0.88[CEU][hapmap]
rs7865648	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831663	chr9:100941048-101109492	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1045780	chr9:100943318-101080389	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv540180	chr9:100943318-101080389	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv831664	chr9:101024862-101205637	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv519818	chr9:101024887-101092316	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101061600-101083400	Weak transcription	Brain Angular Gyrus	brain
2	chr9:101069000-101085800	Weak transcription	Right Atrium	heart
3	chr9:101075400-101082200	Enhancers	K562	blood
4	chr9:101076400-101078600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:101076400-101078600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:101076400-101079800	Enhancers	Placenta	Placenta
7	chr9:101076600-101078400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr9:101076800-101078400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:101076800-101078400	Enhancers	NHDF-Ad	bronchial
10	chr9:101077000-101078400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:101077000-101078400	Enhancers	Fetal Intestine Large	intestine
12	chr9:101077000-101078400	Enhancers	Lung	lung
13	chr9:101077200-101078400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:101077400-101079200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:101077400-101081200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:101077600-101080400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:101077800-101078400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr9:101077800-101078400	Enhancers	Fetal Intestine Small	intestine
19	chr9:101077800-101078800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr9:101077800-101079000	Enhancers	Liver	Liver
21	chr9:101078000-101078400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr9:101078000-101078400	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr9:101078000-101078400	Enhancers	Fetal Brain Male	brain
24	chr9:101078000-101078400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr9:101078000-101078400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
26	chr9:101078000-101078400	Enhancers	HepG2	liver
27	chr9:101078000-101078600	Enhancers	Fetal Muscle Leg	muscle
28	chr9:101078000-101078600	Enhancers	NH-A	brain
29	chr9:101078000-101078600	Enhancers	NHLF	lung
30	chr9:101078000-101079200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr9:101078000-101079400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr9:101078000-101080400	Enhancers	HUVEC	blood vessel
33	chr9:101078200-101078400	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr9:101078200-101078400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:101078200-101078400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr9:101078200-101079000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:101078200-101080000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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