Variant report

Variant	rs4467961
Chromosome Location	chr8:118925538-118925539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:118924992..118927722-chr8:118950419..118952468,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10098363	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10110572	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs1125103	0.80[CEU][hapmap]
rs11777220	0.95[EUR][1000 genomes]
rs11780699	0.80[CEU][hapmap]
rs11781245	0.80[CEU][hapmap]
rs13251463	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13251971	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs13252084	0.82[JPT][hapmap]
rs13266866	0.90[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap]
rs13275942	0.90[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.81[YRI][hapmap];0.80[ASN][1000 genomes]
rs13280053	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1542519	0.84[CEU][hapmap];0.92[GIH][hapmap];0.82[EUR][1000 genomes]
rs2447537	0.80[CEU][hapmap]
rs2447538	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2447539	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2447540	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs2447541	0.84[CEU][hapmap];0.92[GIH][hapmap];0.81[EUR][1000 genomes]
rs2514720	0.80[CEU][hapmap]
rs3101574	0.80[CEU][hapmap]
rs3860883	0.91[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4298514	0.80[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs4480148	0.81[JPT][hapmap]
rs4541958	0.80[CEU][hapmap];0.85[GIH][hapmap]
rs4621831	0.82[JPT][hapmap]
rs4644291	0.81[ASN][1000 genomes]
rs4876769	0.80[ASN][1000 genomes]
rs4876771	0.96[CEU][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4876774	0.84[CEU][hapmap];0.81[CHB][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4876775	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs4876783	0.87[GIH][hapmap]
rs4876784	0.85[GIH][hapmap]
rs6469715	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs6469718	0.80[CEU][hapmap];0.81[ASN][1000 genomes]
rs6981592	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs6990519	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs7002023	0.90[CHB][hapmap]
rs7014561	0.90[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs7812722	0.87[CEU][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.83[EUR][1000 genomes]
rs7814022	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs7841914	0.90[CHB][hapmap]
rs958381	0.80[CEU][hapmap];0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019636	chr8:118598433-118946091	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv539734	chr8:118598433-118946091	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv933516	chr8:118764605-119009093	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1030459	chr8:118840179-119155835	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv831440	chr8:118871930-119052269	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv891411	chr8:118891896-118942698	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1032355	chr8:118896733-119003223	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv465785	chr8:118901928-118970300	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv612046	chr8:118901928-118970300	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4467961	MAL2	cis	cerebellum	SCAN
rs4467961	NOV	cis	cerebellum	SCAN
rs4467961	SNTB1	cis	parietal	SCAN
rs4467961	MED30	cis	parietal	SCAN
rs4467961	NOBOX	trans	multi-tissue	Pritchard

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:118908800-118925800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr8:118912000-118925800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr8:118913400-118925600	Weak transcription	Colon Smooth Muscle	Colon
4	chr8:118916200-118925800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr8:118919000-118926800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr8:118919200-118933200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr8:118919800-118925800	Weak transcription	Small Intestine	intestine
8	chr8:118921200-118926400	Enhancers	NHDF-Ad	bronchial
9	chr8:118921200-118926600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr8:118921600-118926400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr8:118921800-118926400	Enhancers	NHLF	lung
12	chr8:118922400-118926400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr8:118922800-118932800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr8:118922800-118934800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr8:118923000-118926600	Enhancers	Muscle Satellite Cultured Cells	--
16	chr8:118923200-118925600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr8:118923200-118926400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr8:118923200-118926400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr8:118923200-118933000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr8:118923600-118926800	Enhancers	Osteobl	bone
21	chr8:118923800-118930000	Weak transcription	Pancreas	Pancrea
22	chr8:118923800-118933800	Weak transcription	Fetal Stomach	stomach
23	chr8:118924000-118925800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr8:118924000-118925800	Weak transcription	A549	lung
25	chr8:118924000-118925800	Weak transcription	NHEK	skin
26	chr8:118924000-118932800	Weak transcription	Ovary	ovary
27	chr8:118924000-118933000	Weak transcription	Lung	lung
28	chr8:118924800-118925800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr8:118924800-118926400	Enhancers	HSMM	muscle
30	chr8:118924800-118926600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr8:118925000-118926400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr8:118925000-118927000	Weak transcription	Liver	Liver
33	chr8:118925000-118927800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr8:118925200-118925800	Enhancers	Aorta	Aorta
35	chr8:118925400-118925600	Flanking Active TSS	NH-A	brain
36	chr8:118925400-118926000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr8:118925400-118926000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr8:118925400-118926000	Enhancers	Rectal Smooth Muscle	rectum
39	chr8:118925400-118926000	Enhancers	HSMMtube	muscle
40	chr8:118925400-118926400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr8:118925400-118926400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr8:118925400-118926400	Enhancers	HMEC	breast

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