Variant report

Variant	rs946987
Chromosome Location	chr10:99276108-99276109
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:99270070..99271608-chr10:99274562..99276590,2	MCF-7	breast:
2	chr10:99275210..99277389-chr10:99300331..99302181,2	MCF-7	breast:
3	chr10:99275579..99277366-chr10:99277998..99279617,2	MCF-7	breast:
4	chr10:99256475..99261666-chr10:99270366..99276913,12	MCF-7	breast:
5	chr10:99214290..99216279-chr10:99275000..99277562,2	K562	blood:
6	chr10:99275110..99276850-chr10:99307857..99310053,2	MCF-7	breast:
7	chr10:99275538..99279686-chr10:99333593..99336127,3	MCF-7	breast:
8	chr10:99256742..99258905-chr10:99274226..99276132,2	K562	blood:
9	chr10:99275110..99276891-chr10:99277737..99279541,2	MCF-7	breast:
10	chr10:99262782..99264844-chr10:99274125..99276549,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000171307	Chromatin interaction
ENSG00000165886	Chromatin interaction
ENSG00000155229	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10732779	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732780	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10736118	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10786353	0.88[JPT][hapmap]
rs10882949	0.81[MKK][hapmap]
rs11189254	0.82[CHB][hapmap]
rs17107905	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs17112803	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs2275588	0.85[CHD][hapmap]
rs3814552	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs4418736	0.84[CHD][hapmap]
rs4919098	0.83[CHD][hapmap]
rs4919103	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6584131	1.00[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6584132	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7089713	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7912825	0.86[CHD][hapmap]
rs928604	0.84[CHD][hapmap]
rs946984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs946985	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs946986	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964733	0.84[CHD][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
rs946987	RRP12	cis	parietal	SCAN
rs946987	MMS19	cis	parietal	SCAN
rs946987	SLC12A7	trans	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99260200-99276800	Weak transcription	Pancreas	Pancrea
2	chr10:99260800-99276800	Weak transcription	HSMM	muscle
3	chr10:99263600-99277800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr10:99263800-99277200	Weak transcription	HSMMtube	muscle
5	chr10:99263800-99277600	Weak transcription	Aorta	Aorta
6	chr10:99266200-99277600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr10:99266600-99277400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr10:99268400-99278200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr10:99268600-99276600	Weak transcription	HMEC	breast
10	chr10:99268600-99277600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr10:99268600-99277600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr10:99268600-99277800	Weak transcription	NHLF	lung
13	chr10:99268800-99276600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr10:99268800-99276600	Weak transcription	HUVEC	blood vessel
15	chr10:99268800-99277000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr10:99268800-99277400	Weak transcription	NH-A	brain
17	chr10:99268800-99277800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr10:99269000-99277000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr10:99269000-99277600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr10:99269400-99276600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr10:99270800-99286200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr10:99271200-99279200	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr10:99271400-99277400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr10:99272200-99277400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr10:99272200-99277400	Weak transcription	Brain Angular Gyrus	brain
26	chr10:99272200-99277600	Weak transcription	Colon Smooth Muscle	Colon
27	chr10:99272600-99276800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr10:99272600-99277200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr10:99272600-99277400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr10:99272600-99277400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr10:99272600-99277600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr10:99272800-99276600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr10:99273000-99277400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr10:99273200-99276600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr10:99273200-99277400	Weak transcription	NHEK	skin
36	chr10:99273200-99277800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr10:99273200-99277800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr10:99273600-99276200	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr10:99273800-99283200	Enhancers	Fetal Muscle Leg	muscle
40	chr10:99273800-99283200	Enhancers	Left Ventricle	heart
41	chr10:99274200-99276200	Enhancers	Brain Cingulate Gyrus	brain
42	chr10:99274200-99279600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr10:99274200-99285000	Enhancers	Right Ventricle	heart
44	chr10:99274400-99276200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr10:99274400-99277600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr10:99274400-99280200	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr10:99274600-99279800	Enhancers	Brain Substantia Nigra	brain
48	chr10:99274800-99276200	Enhancers	Brain Hippocampus Middle	brain
49	chr10:99274800-99279000	Enhancers	Fetal Muscle Trunk	muscle
50	chr10:99274800-99279400	Enhancers	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links