Variant report

Variant	rs4979261
Chromosome Location	chr9:116355415-116355416
allele	A/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	WRNIP1	chr9:116355396-116355483	GM12878	blood:	n/a	n/a
2	EP300	chr9:116355302-116355799	GM12878	blood:	n/a	chr9:116355661-116355675 chr9:116355655-116355669
3	MAFK	chr9:116355276-116356292	HepG2	liver:	n/a	chr9:116355675-116355684 chr9:116355677-116355688 chr9:116355673-116355688 chr9:116355678-116355689 chr9:116355678-116355689 chr9:116355676-116355690 chr9:116355677-116355688 chr9:116355673-116355689

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:116353757..116355590-chr9:116411695..116413672,3	MCF-7	breast:
2	chr9:116036733..116038262-chr9:116353878..116356485,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237073	TF binding region
RGS3	TF binding region
ENSG00000136875	Chromatin interaction
ENSG00000176386	Chromatin interaction
ENSG00000227482	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10739393	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981836	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12350531	0.85[JPT][hapmap]
rs12685417	0.92[JPT][hapmap]
rs12686023	0.92[JPT][hapmap]
rs14419	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs17187621	0.85[JPT][hapmap]
rs4979253	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];0.89[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs518636	0.85[JPT][hapmap]
rs818714	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893747	chr9:116214058-116386438	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS 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	13 gene(s)	inside rSNPs	diseases
3	nsv466508	chr9:116244982-116362738	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv615215	chr9:116244982-116362738	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv526579	chr9:116244982-116391162	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv893748	chr9:116308709-116421786	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS 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	13 gene(s)	inside rSNPs	diseases
7	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4979261	ALAD	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116341600-116355800	Weak transcription	Fetal Brain Female	brain
2	chr9:116343200-116358800	Weak transcription	Hela-S3	cervix
3	chr9:116346600-116356800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr9:116346800-116355800	Weak transcription	Brain Germinal Matrix	brain
5	chr9:116346800-116356000	Weak transcription	Ovary	ovary
6	chr9:116347200-116355800	Weak transcription	HSMMtube	muscle
7	chr9:116348000-116361600	Weak transcription	Dnd41	blood
8	chr9:116348200-116356400	Weak transcription	Aorta	Aorta
9	chr9:116348400-116355600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr9:116348600-116355600	Weak transcription	HMEC	breast
11	chr9:116348600-116355800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:116349000-116355800	Enhancers	Adipose Nuclei	Adipose
13	chr9:116349000-116355800	Weak transcription	Fetal Intestine Large	intestine
14	chr9:116349600-116355600	Weak transcription	Osteobl	bone
15	chr9:116350000-116355800	Weak transcription	HSMM	muscle
16	chr9:116350600-116355800	Weak transcription	Colonic Mucosa	Colon
17	chr9:116351400-116355800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr9:116351600-116355800	Enhancers	Primary hematopoietic stem cells	blood
19	chr9:116351800-116355600	Weak transcription	Primary B cells from cord blood	blood
20	chr9:116352200-116355800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr9:116352200-116355800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:116352200-116355800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr9:116352200-116357400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr9:116352400-116355800	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr9:116352400-116355800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr9:116352400-116355800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:116352400-116357000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr9:116352400-116357600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr9:116352400-116358000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr9:116352400-116363200	Weak transcription	Thymus	Thymus
31	chr9:116352600-116357000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr9:116353200-116361000	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr9:116353200-116361400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr9:116353400-116355800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:116353400-116355800	Strong transcription	Fetal Intestine Small	intestine
36	chr9:116353400-116356200	Enhancers	Fetal Heart	heart
37	chr9:116353400-116356400	Enhancers	Placenta	Placenta
38	chr9:116353400-116361400	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr9:116353600-116355800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr9:116353600-116355800	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr9:116353600-116355800	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr9:116353600-116355800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:116353600-116356000	Enhancers	Brain Hippocampus Middle	brain
44	chr9:116353800-116355800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:116353800-116355800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr9:116353800-116355800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:116353800-116355800	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr9:116353800-116355800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr9:116353800-116355800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr9:116353800-116356000	Enhancers	Liver	Liver

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