Variant report

Variant	rs4876398
Chromosome Location	chr8:119030277-119030278
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	chr8:119022743..119025680-chr8:119028143..119030470,3	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1037693	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955845	0.89[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10955849	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11562667	0.94[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12543161	0.89[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs13261684	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17453854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126630	0.82[TSI][hapmap]
rs2169604	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279121	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.91[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	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
2	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
3	nsv612047	chr8:118939094-119468609	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1015380	chr8:118948652-119418389	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv539736	chr8:118948652-119418389	Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1025002	chr8:118970940-119069418	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4876398	TNFRSF11B	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:118994000-119031000	Weak transcription	Primary T cells from cord blood	blood
2	chr8:119018000-119033200	Weak transcription	Spleen	Spleen
3	chr8:119021800-119036000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr8:119022000-119030400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr8:119024000-119030600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr8:119024200-119038000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr8:119024600-119031600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr8:119024600-119033800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr8:119024800-119031600	Weak transcription	Psoas Muscle	Psoas
10	chr8:119024800-119036000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr8:119024800-119036600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr8:119024800-119037000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr8:119025000-119038200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr8:119025600-119030400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr8:119026000-119031800	Weak transcription	Thymus	Thymus
16	chr8:119026200-119034400	Enhancers	Small Intestine	intestine
17	chr8:119027000-119034400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr8:119028000-119030400	Enhancers	Duodenum Mucosa	Duodenum
19	chr8:119028000-119030800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr8:119028200-119030400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr8:119028200-119030600	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr8:119028200-119031000	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr8:119028600-119030400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr8:119028600-119031000	Flanking Active TSS	HMEC	breast
25	chr8:119028600-119032400	Enhancers	HSMM	muscle
26	chr8:119028800-119032200	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr8:119028800-119032400	Flanking Active TSS	NHEK	skin
28	chr8:119029000-119030400	Enhancers	Hela-S3	cervix
29	chr8:119029000-119032000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr8:119029000-119032200	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr8:119029000-119036000	Weak transcription	Right Ventricle	heart
32	chr8:119029000-119038200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr8:119029200-119030600	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr8:119029200-119030600	Enhancers	Rectal Smooth Muscle	rectum
35	chr8:119029200-119031600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr8:119029200-119031600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr8:119029200-119034400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr8:119029200-119036000	Weak transcription	Esophagus	oesophagus
39	chr8:119029400-119030400	Enhancers	NH-A	brain
40	chr8:119029400-119031000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr8:119029400-119032000	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr8:119029400-119032000	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr8:119029400-119032000	Enhancers	Stomach Mucosa	stomach
44	chr8:119029400-119032000	Enhancers	HepG2	liver
45	chr8:119029600-119030400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr8:119029600-119030600	Enhancers	HUVEC	blood vessel
47	chr8:119029600-119030800	Enhancers	Fetal Muscle Leg	muscle
48	chr8:119029600-119031800	Enhancers	Fetal Kidney	kidney
49	chr8:119029600-119032400	Enhancers	HSMMtube	muscle
50	chr8:119029600-119033600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links