Variant report

Variant	rs4682081
Chromosome Location	chr3:111762518-111762519
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:111762244..111763263-chr3:111830391..111831101,4	MCF-7	breast:
2	chr3:111752540..111756075-chr3:111760637..111763869,3	MCF-7	breast:
3	chr3:111707669..111708446-chr3:111761873..111762679,2	MCF-7	breast:
4	chr3:111757946..111760451-chr3:111761059..111762628,2	MCF-7	breast:
5	chr3:111707963..111708464-chr3:111762324..111763155,2	K562	blood:
6	chr3:111707324..111708507-chr3:111762237..111763099,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176040	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10934131	0.85[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs10934132	0.85[CEU][hapmap]
rs10934133	0.85[CEU][hapmap]
rs11711987	0.85[CEU][hapmap]
rs11713084	0.85[CEU][hapmap]
rs11713897	0.85[CEU][hapmap]
rs11716665	0.85[CEU][hapmap]
rs11720631	0.85[CEU][hapmap]
rs11927988	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs11928025	0.84[CEU][hapmap]
rs12489437	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16859115	0.85[CEU][hapmap]
rs16859126	0.85[CEU][hapmap]
rs17443498	0.85[CEU][hapmap]
rs17502804	0.85[CEU][hapmap]
rs4682351	0.85[CEU][hapmap]
rs4682352	0.82[CEU][hapmap]
rs4682353	0.85[CEU][hapmap]
rs62280175	0.83[EUR][1000 genomes]
rs7622025	0.95[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7625159	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7630245	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs774768	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs920708	0.85[CEU][hapmap]
rs9288935	0.85[CEU][hapmap]
rs9829091	0.83[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4682081	NAA50	cis	parietal	SCAN
rs4682081	CD200	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111754400-111762600	Weak transcription	Fetal Heart	heart
2	chr3:111756200-111763200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:111757600-111767800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:111758200-111763000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:111759600-111762800	Weak transcription	Thymus	Thymus
6	chr3:111759800-111762600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:111760200-111762600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr3:111760600-111766600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:111760600-111767600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:111760600-111767600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:111761400-111763200	Enhancers	Stomach Mucosa	stomach
12	chr3:111761600-111762600	Enhancers	Brain Substantia Nigra	brain
13	chr3:111761600-111762600	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr3:111761600-111762800	Enhancers	Fetal Brain Female	brain
15	chr3:111761600-111763000	Enhancers	Brain Cingulate Gyrus	brain
16	chr3:111761800-111762600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr3:111762000-111762600	Enhancers	Fetal Intestine Large	intestine
18	chr3:111762000-111763000	Active TSS	Brain Angular Gyrus	brain
19	chr3:111762200-111762600	Enhancers	Dnd41	blood
20	chr3:111762200-111763000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:111762200-111763000	Active TSS	Brain Anterior Caudate	brain
22	chr3:111762200-111763000	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr3:111762200-111763000	Enhancers	NHEK	skin
24	chr3:111762200-111763200	Weak transcription	Fetal Intestine Small	intestine
25	chr3:111762200-111764000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:111762400-111762600	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr3:111762400-111762600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:111762400-111762600	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr3:111762400-111762600	Enhancers	Muscle Satellite Cultured Cells	--
30	chr3:111762400-111762800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:111762400-111762800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:111762400-111763000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr3:111762400-111763000	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr3:111762400-111763000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:111762400-111763000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:111762400-111763000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:111762400-111763000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:111762400-111763000	Active TSS	Adipose Nuclei	Adipose
39	chr3:111762400-111763000	Enhancers	Liver	Liver
40	chr3:111762400-111763000	Active TSS	Brain Hippocampus Middle	brain
41	chr3:111762400-111763000	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr3:111762400-111763000	Active TSS	Right Atrium	heart
43	chr3:111762400-111763000	Active TSS	A549	lung
44	chr3:111762400-111763000	Enhancers	HMEC	breast
45	chr3:111762400-111763000	Enhancers	NH-A	brain
46	chr3:111762400-111763000	Active TSS	NHLF	lung
47	chr3:111762400-111763000	Active TSS	Osteobl	bone
48	chr3:111762400-111763400	Enhancers	Fetal Thymus	thymus
49	chr3:111762400-111763800	Enhancers	HUVEC	blood vessel
50	chr3:111762400-111771000	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links