Variant report

Variant	rs4133101
Chromosome Location	chr5:40679567-40679568
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10060234	0.88[CEU][hapmap]
rs171605	0.88[CEU][hapmap]
rs249414	0.88[CEU][hapmap]
rs249422	0.88[CEU][hapmap]
rs249425	0.88[CEU][hapmap]
rs29742	0.87[CEU][hapmap]
rs29743	0.88[CEU][hapmap]
rs29744	0.88[CEU][hapmap]
rs4314453	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs434778	0.88[CEU][hapmap]
rs4383756	0.88[CEU][hapmap]
rs4412150	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4434423	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs447810	0.88[CEU][hapmap]
rs4546432	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4607392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451535	0.88[CEU][hapmap]
rs7726237	0.88[CEU][hapmap]

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	nsv880993	chr5:40521648-40682550	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
2	nsv880539	chr5:40662257-40713645	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	esv3397684	chr5:40678645-40681143	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4133101	LOC100133612	trans	lymphoblastoid	seeQTL
rs4133101	TTC33	Cis_1M	lymphoblastoid	RTeQTL
rs4133101	RPL37	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40677400-40680800	Active TSS	Duodenum Mucosa	Duodenum
2	chr5:40677400-40681000	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr5:40677800-40680200	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr5:40677800-40681000	Active TSS	Rectal Mucosa Donor 31	rectum
5	chr5:40678200-40680400	Active TSS	Stomach Smooth Muscle	stomach
6	chr5:40678200-40680800	Active TSS	Dnd41	blood
7	chr5:40678400-40680800	Active TSS	A549	lung
8	chr5:40678400-40681000	Active TSS	Fetal Intestine Small	intestine
9	chr5:40678400-40681000	Active TSS	Thymus	Thymus
10	chr5:40678400-40681400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:40678400-40682000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:40678400-40683800	Active TSS	HSMM	muscle
13	chr5:40678400-40684600	Active TSS	HSMMtube	muscle
14	chr5:40678600-40680000	Active TSS	H1 Cell Line	embryonic stem cell
15	chr5:40678600-40680400	Active TSS	Colonic Mucosa	Colon
16	chr5:40678600-40680400	Active TSS	Right Ventricle	heart
17	chr5:40678600-40680600	Active TSS	Stomach Mucosa	stomach
18	chr5:40678600-40680800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr5:40678600-40681000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:40678600-40681200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:40678600-40681200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:40678600-40681200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:40678600-40682200	Active TSS	NHEK	skin
24	chr5:40678600-40684400	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr5:40678600-40685800	Active TSS	Right Atrium	heart
26	chr5:40678800-40680200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:40678800-40680200	Active TSS	Fetal Lung	lung
28	chr5:40678800-40680200	Active TSS	Hela-S3	cervix
29	chr5:40678800-40680400	Bivalent/Poised TSS	Psoas Muscle	Psoas
30	chr5:40678800-40680600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
31	chr5:40678800-40680800	Active TSS	HMEC	breast
32	chr5:40678800-40681000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:40678800-40681000	Active TSS	NHDF-Ad	bronchial
34	chr5:40678800-40681200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:40678800-40681200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:40678800-40683000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:40679000-40679800	Bivalent/Poised TSS	Fetal Brain Male	brain
38	chr5:40679000-40680000	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr5:40679000-40680000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr5:40679000-40680000	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr5:40679000-40680000	Active TSS	Placenta Amnion	Placenta Amnion
42	chr5:40679000-40680200	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr5:40679000-40680200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr5:40679000-40680200	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr5:40679000-40680200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr5:40679000-40680200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
47	chr5:40679000-40680200	Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr5:40679000-40680400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr5:40679000-40680400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:40679000-40680400	Active TSS	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links