Variant report

Variant	rs9583490
Chromosome Location	chr13:111048894-111048895
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	chr13:111042974..111045248-chr13:111048592..111050627,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs57407211	1.00[ASN][1000 genomes]
rs57442307	1.00[ASN][1000 genomes]
rs57465067	1.00[ASN][1000 genomes]
rs58303641	1.00[ASN][1000 genomes]
rs58556553	0.84[ASN][1000 genomes]
rs61445463	1.00[ASN][1000 genomes]
rs61659590	1.00[ASN][1000 genomes]
rs61963199	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61963200	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61963201	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61963202	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv2751128	chr13:111040798-111132490	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9583490	TNFRSF1A	trans	lymphoblastoid	seeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111040800-111049600	Enhancers	NHDF-Ad	bronchial
2	chr13:111040800-111050800	Weak transcription	Psoas Muscle	Psoas
3	chr13:111040800-111058000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr13:111041400-111058000	Weak transcription	Fetal Intestine Large	intestine
5	chr13:111043000-111049600	Weak transcription	Right Ventricle	heart
6	chr13:111043000-111057000	Weak transcription	NHEK	skin
7	chr13:111043000-111059200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:111043000-111060000	Weak transcription	A549	lung
9	chr13:111044000-111051000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr13:111044200-111049400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr13:111044800-111049600	Enhancers	Adipose Nuclei	Adipose
12	chr13:111045000-111049600	Enhancers	NHLF	lung
13	chr13:111045200-111056800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr13:111045600-111050000	Weak transcription	Fetal Kidney	kidney
15	chr13:111045600-111054200	Weak transcription	Spleen	Spleen
16	chr13:111045600-111054600	Weak transcription	HUVEC	blood vessel
17	chr13:111045600-111058200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr13:111045600-111059400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr13:111046600-111049000	Enhancers	Ovary	ovary
20	chr13:111046800-111049000	Enhancers	Placenta	Placenta
21	chr13:111046800-111049600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr13:111046800-111049600	Enhancers	Colon Smooth Muscle	Colon
23	chr13:111046800-111049600	Enhancers	Rectal Smooth Muscle	rectum
24	chr13:111046800-111049600	Enhancers	HSMMtube	muscle
25	chr13:111046800-111050200	Enhancers	Lung	lung
26	chr13:111046800-111051600	Enhancers	Left Ventricle	heart
27	chr13:111047200-111049000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr13:111047200-111050000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr13:111047400-111049200	Enhancers	Fetal Lung	lung
30	chr13:111047400-111049400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr13:111047400-111049600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr13:111047800-111049400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr13:111047800-111050600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr13:111048000-111049600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr13:111048200-111049600	Enhancers	Fetal Stomach	stomach
36	chr13:111048200-111049800	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr13:111048200-111050200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr13:111048200-111052200	Enhancers	Fetal Muscle Leg	muscle
39	chr13:111048400-111049000	Enhancers	Aorta	Aorta
40	chr13:111048400-111049200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr13:111048400-111049400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr13:111048400-111049400	Enhancers	HMEC	breast
43	chr13:111048400-111049600	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr13:111048400-111052400	Enhancers	Fetal Heart	heart
45	chr13:111048600-111049000	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr13:111048600-111049200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr13:111048600-111049200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr13:111048600-111049200	Flanking Active TSS	HSMM	muscle
49	chr13:111048600-111049200	Flanking Active TSS	Osteobl	bone
50	chr13:111048600-111049600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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