Variant report

Variant	rs2316264
Chromosome Location	chr3:100123474-100123475
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100116341..100122043-chr3:100122556..100129449,8	MCF-7	breast:
2	chr3:100102691..100105563-chr3:100122980..100125104,2	MCF-7	breast:
3	chr3:100117960..100119967-chr3:100122961..100124652,2	K562	blood:
4	chr3:100120818..100123698-chr3:100370041..100372201,2	K562	blood:

Variant related genes	Relation type
ENSG00000154174	Chromatin interaction
ENSG00000206535	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1214377	0.83[ASN][1000 genomes]
rs1661287	0.87[ASN][1000 genomes]
rs2289500	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs277632	0.87[ASN][1000 genomes]
rs277639	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs277641	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs277647	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6797836	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72941470	0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2316264	FILIP1L	cis	cerebellum	SCAN
rs2316264	TOMM70A	Cis_1M	lymphoblastoid	RTeQTL
rs2316264	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100118200-100123600	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr3:100119200-100124600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:100121000-100127000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:100121000-100127000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:100121000-100127000	Weak transcription	Gastric	stomach
6	chr3:100121400-100124200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr3:100121800-100131000	Weak transcription	Psoas Muscle	Psoas
8	chr3:100122000-100124400	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr3:100122000-100127000	Weak transcription	Aorta	Aorta
10	chr3:100122000-100143800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:100122400-100127000	Weak transcription	Thymus	Thymus
12	chr3:100122400-100132400	Weak transcription	Primary T cells from cord blood	blood
13	chr3:100122600-100123600	Flanking Active TSS	Liver	Liver
14	chr3:100122600-100124400	Weak transcription	Fetal Intestine Large	intestine
15	chr3:100122600-100126200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:100122600-100127000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:100122600-100127000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:100122600-100129800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:100122600-100132400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:100122600-100133600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:100122600-100149200	Weak transcription	Left Ventricle	heart
22	chr3:100122800-100123600	Flanking Active TSS	HepG2	liver
23	chr3:100122800-100126000	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:100122800-100126000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr3:100122800-100126200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr3:100122800-100126400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:100122800-100127000	Weak transcription	Pancreas	Pancrea
28	chr3:100122800-100129800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:100122800-100131600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:100123000-100124200	Enhancers	Hela-S3	cervix
31	chr3:100123000-100129000	Weak transcription	NHLF	lung
32	chr3:100123000-100131600	Weak transcription	Fetal Heart	heart
33	chr3:100123000-100131600	Weak transcription	HSMM	muscle
34	chr3:100123000-100131800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:100123000-100132600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr3:100123000-100133600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:100123200-100123600	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr3:100123200-100124400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:100123200-100126000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:100123200-100126000	Weak transcription	Fetal Lung	lung
41	chr3:100123200-100127000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:100123200-100127000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:100123200-100127000	Weak transcription	Ovary	ovary
44	chr3:100123200-100130200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:100123200-100133600	Weak transcription	A549	lung
46	chr3:100123200-100135400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:100123400-100123600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr3:100123400-100123600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:100123400-100123600	Flanking Active TSS	GM12878-XiMat	blood
50	chr3:100123400-100123800	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links