Variant report

Variant	rs389663
Chromosome Location	chr6:117868051-117868052
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:117826330..117829186-chr6:117866994..117868994,2	MCF-7	breast:
2	chr6:117802435..117804149-chr6:117867844..117870833,3	MCF-7	breast:
3	chr6:117803061..117805228-chr6:117865961..117868143,2	K562	blood:

Variant related genes	Relation type
ENSG00000164465	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11153678	0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs17079404	0.82[CEU][hapmap];0.80[JPT][hapmap]
rs210616	0.82[CEU][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs210618	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs210619	0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs210620	0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs210621	0.86[CEU][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs210625	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs210627	0.82[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs210628	0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs210629	0.85[ASN][1000 genomes]
rs210631	0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs210632	0.84[CHD][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs210634	0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs210636	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs210638	0.82[CEU][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs210643	0.82[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs28650886	0.83[ASN][1000 genomes]
rs4443534	0.82[CEU][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs8088	0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs9320608	0.92[ASN][1000 genomes]
rs9320609	0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs9320611	0.82[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs9387489	0.81[ASN][1000 genomes]
rs9387490	0.83[ASN][1000 genomes]
rs9401015	0.85[ASN][1000 genomes]
rs9401016	0.82[CEU][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9489217	0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs9689805	0.83[ASN][1000 genomes]
rs9689889	0.82[CEU][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs389663	MCM9	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117819800-117868800	Weak transcription	Spleen	Spleen
2	chr6:117821600-117868800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:117823200-117868800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:117823200-117869600	Weak transcription	Small Intestine	intestine
5	chr6:117835200-117868800	Weak transcription	Colonic Mucosa	Colon
6	chr6:117835400-117868800	Weak transcription	Psoas Muscle	Psoas
7	chr6:117836600-117869600	Weak transcription	Stomach Mucosa	stomach
8	chr6:117838600-117869000	Weak transcription	Ovary	ovary
9	chr6:117845800-117868800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:117846800-117869600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:117851800-117868800	Weak transcription	Right Ventricle	heart
12	chr6:117853200-117868600	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr6:117853200-117868600	Strong transcription	HSMM	muscle
14	chr6:117853400-117868800	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:117853400-117868800	Weak transcription	NHDF-Ad	bronchial
16	chr6:117853600-117868600	Strong transcription	Osteobl	bone
17	chr6:117853600-117868800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:117854200-117868800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:117854400-117868800	Weak transcription	Brain Angular Gyrus	brain
20	chr6:117855000-117868200	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr6:117857000-117869200	Weak transcription	Fetal Kidney	kidney
22	chr6:117857800-117868600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:117858000-117868800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:117858000-117869200	Weak transcription	Placenta	Placenta
25	chr6:117858200-117870400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:117859000-117868800	Strong transcription	Duodenum Mucosa	Duodenum
27	chr6:117859400-117868800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:117859400-117868800	Weak transcription	Brain Anterior Caudate	brain
29	chr6:117859600-117868600	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr6:117859800-117869400	Strong transcription	Fetal Intestine Large	intestine
31	chr6:117860400-117868200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:117860600-117868800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:117860800-117868800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:117861000-117869600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr6:117861400-117868800	Weak transcription	Brain Substantia Nigra	brain
36	chr6:117861400-117869200	Genic enhancers	HMEC	breast
37	chr6:117862200-117868400	Weak transcription	Fetal Muscle Leg	muscle
38	chr6:117862400-117869000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr6:117862800-117869800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr6:117863400-117869200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:117863400-117872200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:117863600-117869000	Strong transcription	Fetal Stomach	stomach
43	chr6:117863600-117869600	Genic enhancers	A549	lung
44	chr6:117863800-117869200	Strong transcription	Fetal Intestine Small	intestine
45	chr6:117864000-117869200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:117864000-117870200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr6:117864600-117868800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:117864600-117868800	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr6:117864800-117868800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:117864800-117868800	Weak transcription	Fetal Brain Male	brain

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