Variant report

Variant	rs7089060
Chromosome Location	chr10:99281793-99281794
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99256542..99259693-chr10:99280360..99283727,3	MCF-7	breast:
2	chr10:99280525..99282276-chr10:99293134..99294655,2	K562	blood:
3	chr10:99280106..99282140-chr10:99290558..99292747,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165886	Chromatin interaction
ENSG00000155229	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10748699	0.83[CHB][hapmap]
rs10882959	0.83[CHB][hapmap]
rs10882962	0.83[CHB][hapmap]
rs11189244	0.86[CHB][hapmap]
rs11189253	0.83[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs11189275	0.83[CHB][hapmap]
rs11189281	0.95[CHB][hapmap]
rs12219064	0.83[CHB][hapmap]
rs12243136	0.87[CHB][hapmap]
rs12415482	0.83[ASN][1000 genomes]
rs1572860	0.83[CHB][hapmap]
rs4917774	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4919104	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4919105	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59109814	0.83[ASN][1000 genomes]
rs7075656	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7902642	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1036494	chr10:99267639-99345207	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7089060	MMS19	cis	parietal	SCAN
rs7089060	MSX1	trans	lymphoblastoid	seeQTL
rs7089060	CC2D2B	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99270800-99286200	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr10:99273800-99283200	Enhancers	Fetal Muscle Leg	muscle
3	chr10:99273800-99283200	Enhancers	Left Ventricle	heart
4	chr10:99274200-99285000	Enhancers	Right Ventricle	heart
5	chr10:99275000-99293800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr10:99276000-99284400	Weak transcription	HepG2	liver
7	chr10:99277200-99282800	Enhancers	HSMMtube	muscle
8	chr10:99277800-99281800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr10:99277800-99301800	Weak transcription	Gastric	stomach
10	chr10:99278000-99302600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr10:99278200-99298800	Weak transcription	Aorta	Aorta
12	chr10:99278400-99281800	Weak transcription	Esophagus	oesophagus
13	chr10:99278400-99289600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr10:99278400-99301800	Weak transcription	Spleen	Spleen
15	chr10:99278600-99281800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr10:99278600-99284400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr10:99278600-99300200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr10:99278800-99281800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr10:99278800-99284400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr10:99279000-99284400	Weak transcription	Ovary	ovary
21	chr10:99279400-99281800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr10:99279400-99284600	Weak transcription	Adipose Nuclei	Adipose
23	chr10:99279600-99282000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr10:99279600-99284000	Enhancers	Right Atrium	heart
25	chr10:99279800-99282000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr10:99279800-99282000	Weak transcription	Brain Substantia Nigra	brain
27	chr10:99279800-99282200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr10:99279800-99283800	Weak transcription	Brain Hippocampus Middle	brain
29	chr10:99279800-99284600	Weak transcription	Brain Angular Gyrus	brain
30	chr10:99279800-99287200	Enhancers	Lung	lung
31	chr10:99280200-99282000	Enhancers	H1 Cell Line	embryonic stem cell
32	chr10:99280200-99284600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr10:99280400-99282000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr10:99280400-99282200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr10:99280400-99282200	Enhancers	Pancreas	Pancrea
36	chr10:99280400-99283000	Enhancers	Fetal Muscle Trunk	muscle
37	chr10:99280600-99283000	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr10:99281200-99281800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr10:99281200-99282000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr10:99281200-99282200	Enhancers	Psoas Muscle	Psoas
41	chr10:99281200-99291400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr10:99281400-99282200	Enhancers	Brain Cingulate Gyrus	brain
43	chr10:99281400-99282600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr10:99281400-99282800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr10:99281400-99302200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr10:99281600-99282200	Enhancers	Fetal Lung	lung
47	chr10:99281600-99282600	Enhancers	Brain Anterior Caudate	brain
48	chr10:99281600-99282600	Enhancers	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links