Variant report

Variant	rs9999978
Chromosome Location	chr4:120981638-120981639
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120981267..120985179-chr4:120986108..120989816,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250938	Chromatin interaction
ENSG00000164109	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10004470	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10004481	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009560	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17010263	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011007	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2055744	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28429746	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28472949	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7685337	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9990631	0.87[EUR][1000 genomes];1.00[ASN][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	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv1007641	chr4:120884220-121555889	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv537234	chr4:120884220-121555889	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv879851	chr4:120942372-120984077	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9999978	GAS7	trans	lymphoblastoid	seeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120962200-120987200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:120971000-120983200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr4:120971000-120987400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:120971200-120983200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:120971200-120985200	Weak transcription	Fetal Kidney	kidney
6	chr4:120971200-120985600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:120971200-120986400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr4:120971200-120986400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr4:120971200-120986800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:120971200-120987200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:120971200-120987200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr4:120971200-120987400	Weak transcription	Left Ventricle	heart
13	chr4:120974200-120984000	Weak transcription	Brain Germinal Matrix	brain
14	chr4:120974400-120983200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr4:120974800-120983600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:120974800-120983800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr4:120974800-120984000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:120974800-120984000	Weak transcription	NHLF	lung
19	chr4:120974800-120985200	Weak transcription	NHEK	skin
20	chr4:120975000-120983400	Weak transcription	NHDF-Ad	bronchial
21	chr4:120975000-120984000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr4:120975000-120985400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:120975000-120985400	Weak transcription	Fetal Stomach	stomach
24	chr4:120975000-120985600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:120975400-120984200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:120975400-120986800	Weak transcription	Primary B cells from cord blood	blood
27	chr4:120975600-120984800	Strong transcription	Fetal Thymus	thymus
28	chr4:120975800-120985400	Weak transcription	Primary T cells from cord blood	blood
29	chr4:120975800-120986800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr4:120976200-120985200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:120976200-120985200	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr4:120976200-120985600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:120976400-120984400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr4:120976400-120985400	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr4:120976600-120983400	Weak transcription	HepG2	liver
36	chr4:120977400-120985400	Weak transcription	Fetal Lung	lung
37	chr4:120977400-120986600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:120977400-120986600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr4:120977400-120986800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr4:120977400-120987200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr4:120978000-120985200	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr4:120978000-120985400	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr4:120978200-120982400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:120978200-120984000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:120978200-120984200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr4:120978200-120987200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:120978400-120982400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr4:120978400-120982600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr4:120978400-120984200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr4:120978400-120986600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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