Variant report

Variant	rs2169604
Chromosome Location	chr8:119024638-119024639
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:
2	chr8:119016095..119018020-chr8:119023255..119025227,2	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1037693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955845	0.94[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs11562667	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12543161	0.94[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs13261684	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17453854	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126630	0.82[TSI][hapmap]
rs2279121	0.94[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4876398	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]

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
rs2169604	TNFRSF11B	cis	cerebellum	SCAN

Chromatin state (count:89 , 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	chr8:119013200-119030000	Weak transcription	Colonic Mucosa	Colon
3	chr8:119016200-119026000	Enhancers	Liver	Liver
4	chr8:119018000-119033200	Weak transcription	Spleen	Spleen
5	chr8:119020000-119024800	Enhancers	Adipose Nuclei	Adipose
6	chr8:119020000-119025600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr8:119020200-119025200	Enhancers	Left Ventricle	heart
8	chr8:119020200-119026000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr8:119020600-119025200	Enhancers	Fetal Heart	heart
10	chr8:119020600-119025400	Enhancers	HSMM	muscle
11	chr8:119020600-119025600	Enhancers	Right Atrium	heart
12	chr8:119020800-119024800	Enhancers	Fetal Lung	lung
13	chr8:119021000-119024800	Enhancers	HSMMtube	muscle
14	chr8:119021000-119026000	Enhancers	Hela-S3	cervix
15	chr8:119021200-119024800	Enhancers	Psoas Muscle	Psoas
16	chr8:119021200-119025600	Enhancers	Ovary	ovary
17	chr8:119021200-119028000	Enhancers	HMEC	breast
18	chr8:119021600-119024800	Enhancers	H1 Cell Line	embryonic stem cell
19	chr8:119021600-119028600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr8:119021600-119030200	Weak transcription	Brain Germinal Matrix	brain
21	chr8:119021800-119024800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr8:119021800-119027800	Weak transcription	Brain Anterior Caudate	brain
23	chr8:119021800-119029600	Weak transcription	Fetal Intestine Large	intestine
24	chr8:119021800-119036000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr8:119022000-119025400	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr8:119022000-119030000	Weak transcription	Fetal Intestine Small	intestine
27	chr8:119022000-119030400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr8:119022200-119028000	Weak transcription	Esophagus	oesophagus
29	chr8:119022400-119025600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr8:119022600-119025000	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr8:119022600-119025000	Enhancers	Fetal Muscle Leg	muscle
32	chr8:119022600-119025200	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr8:119022600-119025200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr8:119022600-119026000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr8:119022800-119024800	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr8:119022800-119024800	Enhancers	Aorta	Aorta
37	chr8:119022800-119025000	Enhancers	Colon Smooth Muscle	Colon
38	chr8:119022800-119025000	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr8:119022800-119025600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr8:119022800-119025800	Enhancers	Placenta	Placenta
41	chr8:119023000-119024800	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr8:119023000-119024800	Enhancers	Fetal Stomach	stomach
43	chr8:119023000-119025000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr8:119023000-119025600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr8:119023000-119025600	Enhancers	Placenta Amnion	Placenta Amnion
46	chr8:119023200-119024800	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr8:119023200-119024800	Enhancers	Stomach Mucosa	stomach
48	chr8:119023200-119024800	Flanking Active TSS	NH-A	brain
49	chr8:119023200-119025200	Enhancers	Duodenum Mucosa	Duodenum
50	chr8:119023200-119025600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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