Variant report

Variant	rs4979439
Chromosome Location	chr9:117351829-117351830
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:117251302..117252928-chr9:117351166..117353449,2	K562	blood:
2	chr9:117346842..117352204-chr9:117370877..117374909,8	K562	blood:
3	chr9:117310558..117329379-chr9:117338511..117355772,81	MCF-7	breast:
4	chr9:117349294..117352043-chr9:117375229..117380114,4	MCF-7	breast:
5	chr9:117163972..117166218-chr9:117350141..117352185,2	MCF-7	breast:
6	chr9:117265762..117270088-chr9:117348229..117352933,7	K562	blood:
7	chr9:117348104..117352194-chr9:117371141..117379325,14	K562	blood:
8	chr9:117264226..117271307-chr9:117346303..117355535,28	MCF-7	breast:
9	chr9:117346757..117362857-chr9:117372020..117377914,21	MCF-7	breast:
10	chr9:117350512..117352142-chr9:117376353..117378083,2	K562	blood:
11	chr9:117351003..117352705-chr9:134269477..134271266,2	MCF-7	breast:
12	chr9:117349427..117352163-chr9:117404465..117406175,2	MCF-7	breast:
13	chr9:117286668..117289203-chr9:117350416..117352540,2	MCF-7	breast:
14	chr9:117264854..117270088-chr9:117348300..117353117,7	K562	blood:
15	chr9:117264990..117269271-chr9:117348762..117354798,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000157693	Chromatin interaction
ENSG00000130723	Chromatin interaction
ENSG00000272241	Chromatin interaction
ENSG00000238530	Chromatin interaction
ENSG00000201749	Chromatin interaction
ENSG00000095397	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10817638	0.80[MKK][hapmap];0.81[TSI][hapmap]
rs10817640	0.83[ASW][hapmap];0.87[CEU][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs10982295	0.85[EUR][1000 genomes]
rs10982299	0.83[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7871401	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422396	chr9:116792944-117354862	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
2	esv2422492	chr9:116811294-117366643	Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
3	nsv1051544	chr9:116944940-117443031	ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
4	nsv540203	chr9:116944940-117443031	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv1048093	chr9:116945025-117456210	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
6	nsv1050991	chr9:116953739-117442999	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv1046311	chr9:116953739-117447142	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
8	nsv1052877	chr9:116953739-117456210	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
9	nsv1039681	chr9:116953739-117457158	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
10	nsv1051987	chr9:116955841-117453668	Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
11	nsv1044374	chr9:116955841-117460150	Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
12	nsv466534	chr9:116956268-117455810	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
13	nsv615234	chr9:116956268-117455810	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
14	nsv1048817	chr9:116957958-117456210	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
15	nsv615235	chr9:116958144-117367061	ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
16	nsv615236	chr9:116958144-117455810	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
17	nsv466535	chr9:116958144-117456175	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
18	nsv615237	chr9:116958144-117456175	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
19	nsv615238	chr9:116958144-117458475	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
20	nsv430094	chr9:116958446-117456446	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
21	nsv1053756	chr9:116975934-117443031	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
22	nsv540204	chr9:116975934-117443031	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
23	nsv1047704	chr9:116978041-117399362	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
24	nsv540205	chr9:116978041-117399362	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
25	nsv530950	chr9:117009156-117399361	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
26	nsv916139	chr9:117009169-117399454	Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
27	nsv530951	chr9:117032675-117439804	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
28	nsv831694	chr9:117328640-117502785	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4979439	ATP6V1G1	cis	multi-tissue	Pritchard
rs4979439	DNAJC25	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117349400-117352000	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr9:117349400-117352400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:117349600-117352600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:117349800-117352200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:117349800-117352400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:117350000-117352000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
7	chr9:117350200-117352200	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr9:117350200-117352400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:117350200-117352400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr9:117350400-117352400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr9:117350600-117352000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr9:117350600-117352000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr9:117350600-117352000	Flanking Active TSS	Right Ventricle	heart
14	chr9:117350600-117352200	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr9:117350600-117352200	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr9:117350600-117352400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr9:117350600-117352400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:117350600-117352400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:117350600-117352400	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr9:117350800-117352000	Flanking Active TSS	Brain Substantia Nigra	brain
21	chr9:117350800-117352000	Flanking Active TSS	Fetal Brain Male	brain
22	chr9:117350800-117352000	Flanking Active TSS	Fetal Stomach	stomach
23	chr9:117350800-117352000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr9:117350800-117352000	Flanking Active TSS	Osteobl	bone
25	chr9:117350800-117352200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr9:117350800-117352200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
27	chr9:117350800-117352200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr9:117350800-117352200	Flanking Active TSS	HUVEC	blood vessel
29	chr9:117350800-117352400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr9:117350800-117352400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr9:117350800-117352400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:117350800-117352400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr9:117351000-117352000	Flanking Active TSS	Brain Cingulate Gyrus	brain
34	chr9:117351000-117352000	Flanking Active TSS	Fetal Brain Female	brain
35	chr9:117351000-117352000	Enhancers	Spleen	Spleen
36	chr9:117351000-117352000	Transcr. at gene 5' and 3'	K562	blood
37	chr9:117351000-117352200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:117351000-117352200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr9:117351000-117352200	Flanking Active TSS	Liver	Liver
40	chr9:117351000-117352200	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr9:117351000-117352200	Flanking Active TSS	Brain Hippocampus Middle	brain
42	chr9:117351000-117352200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr9:117351000-117352200	Flanking Active TSS	Hela-S3	cervix
44	chr9:117351000-117352200	Flanking Active TSS	NH-A	brain
45	chr9:117351000-117352400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr9:117351000-117352400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr9:117351000-117352400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr9:117351200-117352000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:117351200-117352000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr9:117351200-117352000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell

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