Variant report

Variant	rs7038589
Chromosome Location	chr9:116081449-116081450
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116079992..116082987-chr9:116085261..116087618,2	K562	blood:
2	chr9:116076058..116079132-chr9:116081074..116084162,3	K562	blood:
3	chr9:116074633..116076167-chr9:116080885..116083605,2	K562	blood:
4	chr9:116079156..116083300-chr9:116100482..116103976,4	MCF-7	breast:
5	chr9:116079992..116082987-chr9:116084415..116087618,3	K562	blood:
6	chr9:116079936..116083155-chr9:116131441..116134734,3	MCF-7	breast:
7	chr9:116081121..116082854-chr9:116101346..116104319,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148225	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10817476	0.95[LWK][hapmap]
rs10817483	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs10981729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11787602	0.81[AFR][1000 genomes]
rs11788333	0.87[AFR][1000 genomes]
rs12378096	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12380548	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276775	1.00[ASN][1000 genomes]
rs66747389	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66790147	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026831	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7032611	1.00[ASN][1000 genomes]
rs7860315	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7870848	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs818710	1.00[CHB][hapmap]
rs912247	0.91[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS 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 target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7038589	C9orf91	cis	parietal	SCAN
rs7038589	ZNF618	cis	cerebellum	SCAN
rs7038589	SLC31A1	cis	parietal	SCAN
rs7038589	PRPF4	cis	Thyroid	GTEx
rs7038589	EPB41L4B	cis	cerebellum	SCAN
rs7038589	SLC31A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116055200-116085200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:116056000-116087000	Weak transcription	Thymus	Thymus
3	chr9:116065400-116086800	Weak transcription	Gastric	stomach
4	chr9:116065600-116083400	Weak transcription	Esophagus	oesophagus
5	chr9:116070800-116083800	Weak transcription	Spleen	Spleen
6	chr9:116072000-116085200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:116073800-116101600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr9:116076000-116084600	Weak transcription	HSMMtube	muscle
9	chr9:116076200-116085000	Weak transcription	Placenta	Placenta
10	chr9:116077000-116086800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr9:116077200-116085600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr9:116077400-116082800	Weak transcription	Colonic Mucosa	Colon
13	chr9:116077400-116083800	Strong transcription	Ovary	ovary
14	chr9:116077400-116084000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:116077400-116084200	Strong transcription	Fetal Stomach	stomach
16	chr9:116077400-116101400	Weak transcription	Brain Germinal Matrix	brain
17	chr9:116077400-116101600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:116077800-116082400	Weak transcription	Aorta	Aorta
19	chr9:116077800-116101200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:116078000-116083800	Weak transcription	Primary T cells from cord blood	blood
21	chr9:116078400-116084200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:116078400-116086400	Strong transcription	Stomach Smooth Muscle	stomach
23	chr9:116078600-116082600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:116078600-116083600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr9:116078800-116082200	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr9:116078800-116082800	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr9:116078800-116093600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr9:116079000-116081800	Strong transcription	Fetal Intestine Large	intestine
29	chr9:116079000-116083800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr9:116079000-116084200	Strong transcription	Brain Anterior Caudate	brain
31	chr9:116079000-116094600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr9:116079200-116083600	Strong transcription	Lung	lung
33	chr9:116079200-116084200	Strong transcription	Brain Hippocampus Middle	brain
34	chr9:116079600-116083000	Strong transcription	Brain Cingulate Gyrus	brain
35	chr9:116079600-116086000	Weak transcription	Fetal Brain Female	brain
36	chr9:116079800-116081600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:116079800-116082600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr9:116079800-116083800	Strong transcription	Left Ventricle	heart
39	chr9:116079800-116087600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr9:116080000-116082400	Weak transcription	Fetal Intestine Small	intestine
41	chr9:116080000-116083600	Weak transcription	Fetal Lung	lung
42	chr9:116080200-116082600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr9:116080200-116084000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr9:116080400-116083800	Strong transcription	Colon Smooth Muscle	Colon
45	chr9:116080600-116082800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr9:116080600-116082800	Strong transcription	Brain Substantia Nigra	brain
47	chr9:116080600-116082800	Strong transcription	Fetal Kidney	kidney
48	chr9:116080600-116083800	Strong transcription	Right Ventricle	heart
49	chr9:116080600-116084200	Strong transcription	Liver	Liver
50	chr9:116080600-116085000	Weak transcription	Adipose Nuclei	Adipose

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