Variant report

Variant	rs4442112
Chromosome Location	chr8:99557366-99557367
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:99547855..99550787-chr8:99555161..99557416,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10086870	0.83[JPT][hapmap]
rs10100346	0.81[JPT][hapmap]
rs10101919	0.83[JPT][hapmap]
rs10955177	0.83[JPT][hapmap]
rs10955178	0.82[JPT][hapmap]
rs10955180	0.83[JPT][hapmap]
rs10955181	0.83[JPT][hapmap]
rs10955185	0.83[JPT][hapmap]
rs10955186	0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs10955187	0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs10955188	0.90[ASN][1000 genomes]
rs12541026	0.86[JPT][hapmap]
rs12542022	1.00[JPT][hapmap]
rs12542069	0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs12542758	0.87[CHB][hapmap];0.87[CHD][hapmap];0.90[ASN][1000 genomes]
rs12542931	0.83[JPT][hapmap]
rs12544768	0.83[JPT][hapmap]
rs12547922	0.83[JPT][hapmap]
rs12548477	0.83[JPT][hapmap]
rs12550198	0.83[JPT][hapmap]
rs12677183	0.85[GIH][hapmap]
rs12680490	0.93[ASN][1000 genomes]
rs12680602	0.91[ASN][1000 genomes]
rs13257475	0.83[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13258214	0.92[ASN][1000 genomes]
rs13269932	0.85[GIH][hapmap]
rs13275915	0.85[GIH][hapmap]
rs16892236	0.87[JPT][hapmap]
rs16897061	1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs16897076	0.81[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35447893	0.80[ASN][1000 genomes]
rs3802198	0.83[JPT][hapmap]
rs4131873	0.81[LWK][hapmap]
rs4301421	0.83[JPT][hapmap]
rs4332102	0.81[JPT][hapmap]
rs4370499	1.00[JPT][hapmap]
rs4734407	0.83[JPT][hapmap]
rs4734410	0.85[GIH][hapmap]
rs4735568	0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs4735574	0.85[GIH][hapmap]
rs62535381	0.90[ASN][1000 genomes]
rs62535382	0.89[ASN][1000 genomes]
rs62535383	0.89[ASN][1000 genomes]
rs6651181	0.82[JPT][hapmap]
rs6992925	0.85[GIH][hapmap]
rs7015739	0.83[JPT][hapmap]
rs7016626	1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7815227	0.83[JPT][hapmap]
rs7816638	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7818010	0.91[CHB][hapmap];0.91[ASN][1000 genomes]
rs7845395	0.83[JPT][hapmap]
rs9656842	0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027362	chr8:99469281-99715845	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv539689	chr8:99469281-99715845	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv891218	chr8:99507313-99906221	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv891219	chr8:99526819-99643487	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv611808	chr8:99544765-99591736	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv1030498	chr8:99545493-99607093	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4442112	RPL30	cis	parietal	SCAN
rs4442112	OSR2	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99500400-99558800	Weak transcription	Aorta	Aorta
2	chr8:99525800-99576400	Weak transcription	Pancreas	Pancrea
3	chr8:99531000-99569600	Weak transcription	HMEC	breast
4	chr8:99531200-99561800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr8:99531400-99586400	Weak transcription	HSMM	muscle
6	chr8:99531600-99561800	Weak transcription	Esophagus	oesophagus
7	chr8:99533400-99566400	Weak transcription	NHLF	lung
8	chr8:99534600-99567200	Weak transcription	A549	lung
9	chr8:99535400-99571600	Weak transcription	Gastric	stomach
10	chr8:99543000-99566800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr8:99544000-99559000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr8:99544000-99560800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr8:99544000-99566800	Weak transcription	Brain Substantia Nigra	brain
14	chr8:99544200-99558800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr8:99544200-99559400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr8:99544600-99560000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr8:99544600-99587000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr8:99546000-99571600	Weak transcription	Fetal Intestine Small	intestine
19	chr8:99546600-99576400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr8:99548400-99560800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr8:99548600-99557400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr8:99548600-99558800	Weak transcription	HSMMtube	muscle
23	chr8:99548600-99569800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr8:99548800-99563400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr8:99549600-99557400	Weak transcription	Osteobl	bone
26	chr8:99549800-99568200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr8:99550000-99557400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr8:99550000-99558200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr8:99550800-99560200	Weak transcription	Right Ventricle	heart
30	chr8:99551000-99557800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr8:99551200-99558800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr8:99551200-99559400	Weak transcription	Small Intestine	intestine
33	chr8:99551200-99560400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr8:99551200-99561800	Weak transcription	Brain Angular Gyrus	brain
35	chr8:99551400-99566000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr8:99551800-99557400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr8:99551800-99562000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr8:99552000-99572600	Weak transcription	Brain Hippocampus Middle	brain
39	chr8:99552600-99559800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr8:99552800-99559000	Weak transcription	GM12878-XiMat	blood
41	chr8:99553000-99559600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr8:99553200-99558600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr8:99553400-99559400	Weak transcription	HepG2	liver
44	chr8:99553400-99560800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr8:99553400-99569600	Weak transcription	Fetal Lung	lung
46	chr8:99553400-99586000	Weak transcription	Ovary	ovary
47	chr8:99553600-99589600	Weak transcription	Fetal Stomach	stomach
48	chr8:99553800-99558600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr8:99553800-99558800	Weak transcription	Liver	Liver
50	chr8:99553800-99561800	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links